110 research outputs found

    A combined genome-wide approach identifies a new potential candidate marker associated with the coat color sidedness in cattle

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    Coat color is one of the most important phenotypic features in livestock breeds. Cinisara is a local cattle breed generally of uniform black color which occasionally presents a particular phenotype, with animals typically display a white band along their spine, from the head to the tail, and on the ventral line (color sidedness). Therefore, this breed provides an ideal model to study the genetic components underlying phenotypic variation in coat color. A total of 63 animals, ten with sidedness phenotype and 53 with uniform black color were genotyped with Illumina Bovine 50 K. The comparison among genome-wide association study and FST analysis revealed a single nucleotide polymorphism (SNP), ARS-BFGL-NGS-55928, significantly associated with the trait. Only one gene (PLK2)was annotated near the associated SNP in a window of ±200 kb. The protein encoded by this gene is a member of the polo-like kinases, the same family of several known coat-color candidate genes. Based on the reported results, we draw the possible conclusion that the identified marker is potentially associated with the coat color sidedness in Cinisara. The local breeds with their genetic variability represent an important resource and model to study the genetic basis affecting peculiar traits. Future studies would be particularly relevant to refine these results and to better understand the genetic basis for this phenotype

    Phenotypic and genetic analysis of udder health using SCC in Valle del Belice dairy sheep

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    Intramammary infections (IMI) are a complex of inflammatory diseases which are defined as an inflammation of the mammary gland resulting from the introduction and multiplication of pathogenic micro-organisms

    Maedi Visna virus infection and TMEM154 genotypes in Valle del Belìce sheep breed

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    Maedi Visna (MV) is a viral infection in sheep caused by Lentivirus and characterised by a long incubation period, slow progression, weight loss and eventually death. TMEM154 was reported in the ovine as major candidate gene associated with host susceptibility/resistance. The aim of this study was to verify the prevalence of MV infection within Sicilian herds of Valle del Belìce breed using an ELISA serological test and to estimate the frequencies of the resistant/susceptible genotypes to the TMEM154 gene. Finally, we investigated the association between TMEM154 E/K genotype and MV infectious status. A total of 1,083 animals from different flocks were tested. The ELISA method showed 15.33% (n = 166) of infected individuals. Analyses of the sequences showed the presence of both K and E alleles with frequencies of 0.151 and 0.849, respectively. On the total individuals, only 23 carried KK genotype while 280 were heterozigous EK, and 780 homozygous EE. The locus was in Hardy-Weinberg equilibrium in the breed (p-value <0.05) and observed and expected heterozygosity values were 0.258 and 0.256, respectively. Moreover, a significant association (p-value < 0.001) between TMEM154 genotypes and seroprevalence status (positive vs. negative) was found. This study allowed us to know the prevalence of MV infection in Sicilian flocks of Valle del Belìce breed and could be helpful in establishing selection programs aimed at controlling and eradicating this virus

    Effect of heat stress on production in Mediterranean dairy sheep

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    European Mediterranean countries are characterized by exposure to considerable heat between three and six months annually. High ambient temperature, solar radiation, wind speed and relative humidity, cause the effective temperature of the environment to be above the thermo-neutral zone of the animals (5 to 25ºC; McDowell, 1972) and therefore heat stress occurs (Bianca, 1962)

    Genome-wide association study for milk production traits in an economically important local dairy sheep breed

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    In this study, we conducted a genome-wide association study (GWAS) for five milk production traits in the Valle del Belice sheep. Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY) on 481 ewes, were available for the analysis. The animals were genotyped using the Illumina Ovine 50k BeadChip. Weighted deregressed breeding values (DEBVw) were used as phenotypes for GWAS analysis. A total of 23 genome-wide significant SNPs were identified: 3 associated with MY, 9 with FY, and 11 with P%. Several SNPs mapped within known candidate genes or previously reported QTL for milk production traits in livestock species. Additional interesting markers were identified on OAR3 for FY and P%. These SNPs supported some previous findings and also added new information useful to understand the genetic mechanisms underlying the milk production and quality traits in dairy sheep.Highlights A total of 23 significant SNPs were detected. Several SNPs mapped within known candidate genes or previously reported QTL for milk production traits. These results could provide information to understand the genetic architecture of milk production traits in dairy sheep

    Genomic structural diversity in local goats: Analysis of copy-number variations

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    Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell’Etna, Derivata di Siria, Girgentana, and Messinese), genotyped with the Illumina GoatSNP50 BeadChip array. Overall, 702 CNVs were identified in 107 individuals using PennCNV software based on the hidden Markov model algorithm. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair, while 85 CNVs remained unique. The part of the genome covered by CNV events was 35.21 Mb (1.2% of the goat genome length). Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs that are involved in local adaptations, such as coat colour (ADAMTS20 and EDNRA), mild behaviour (NR3C2), immune response (EXOC3L4 and TNFAIP2), reproduction (GBP1 and GBP6), and olfactory receptors (OR7E24). This study provides insights into the genomic variations for these Sicilian dairy goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits

    Genome-Wide Association Study Identifies New Candidate Markers for Somatic Cells Score in a Local Dairy Sheep

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    In the Mediterranean basin countries, the dairy sheep production is usually based on local breeds, which are very well-adapted to their production systems and environments and can indeed guarantee income, employment, and economic viability in areas where production alternatives are scarce or non-existent. Mastitis is still one of the greatest problems affecting commercial milk production. However, genetic evaluation of mastitis is particularly difficult because of its low heritability and the categorical nature of the trait. The aim of this study was to identify genomic regions putatively associated with somatic cells count (SCC) in the local economically important Valle del Belice sheep breed using of deregressed breeding values (DEBV) as response variables. All the samples were genotyped using the Illumina OvineSNP50K BeadChip. Genome-wide association analysis was carried out based on regression of DEBV. A total of eight markers were found to be significantly associated with log-transformed SCC. Several candidate genes associated with SCC were identified related to immunity system and udder conformation. The results can help improving the competitiveness of the local Valle del Belìce breed. Further studies considering a higher sample size or independent population will be needed to confirm our results

    Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

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    Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome

    A genome-wide comparison between selected and unselected Valle del Belice sheep reveals differences in population structure and footprints of recent selection

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    About three decades of breeding and selection in the Valle del Belìce sheep are expected to have left several genomic footprints related to milk production traits. In this study, we have assembled a dataset with 451 individuals of the Valle del Belìce sheep breed: 184 animals that underwent directional selection for milk production and 267 unselected animals, genotyped for 40,660 single-nucleotide polymorphisms (SNPs). Three different statistical approaches, both within (iHS and ROH) and between (Rsb) groups, were used to identify genomic regions potentially under selection. Population structure analyses separated all individuals according to their belonging to the two groups. A total of four genomic regions on two chromosomes were jointly identified by at least two statistical approaches. Several candidate genes for milk production were identified, corroborating the polygenic nature of this trait and which may provide clues to potential new selection targets. We also found candidate genes for growth and reproductive traits. Overall, the identified genes may explain the effect of selection to improve the performances related to milk production traits in the breed. Further studies using high-density array data, would be particularly relevant to refine and validate these results

    A First Investigation into the Use of Differential Somatic Cell Count as a Predictor of Udder Health in Sheep

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    Differential somatic cell count (DSCC), the percentage of somatic cell count (SCC) due to polymorphonuclear leukocytes (PMNs) and lymphocytes (LYMs), is a promising effective diagnostic marker for dairy animals with infected mammary glands. Well-explored in dairy cows, DSCC is also potentially valid in sheep, where clinical and subclinical mastitis outbreaks are among the principal causes of culling. We pioneered the application of DSCC in dairy ewes by applying receiver-operating characteristic (ROC) curve analysis to define the most accurate thresholds to facilitate early discrimination of sheep with potential intramammary infection (IMI) from healthy animals. We tested four predefined SCC cut-offs established in previous research. Specifically, we applied SCC cut-offs of 265 × 103 cells/mL, 500 × 103 cells/mL, 645 × 103 cells/mL, and 1000 × 103 cells/mL. The performance of DSCC as a diagnostic test was assessed by examining sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV), and area under curve (AUC) analyses. The designated threshold value for DSCC in the detection of subclinical mastitis is established at 79.8%. This threshold exhibits Se and Sp of 0.84 and 0.81, accompanied by an AUC of 0.88. This study represents the inaugural exploration of the potential use of DSCC in sheep’s milk as an early indicator of udder inflammation
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