Indagine preliminare sul polimorfismo lattoproteico in diverse popolazioni caprine allevate in Sicilia.

La consistenza del patrimonio caprino in Italia ha subito negliiltimi anni un aumento considerevole. Significativo è stato l’incremento del 6,6% della produzione di latte tra il 2000 e il 2002. Il recente sviluppo dell’allevamento caprino è dovuto in gran parte al crescente interesse dei consumatoru sia verso i prodotti caseari tipici sia verso il consumo diretto del latte. Le caseina caprine sono caratterizzate da un elevato polimorfismo genetico, sia a livello qualitativo che quantitativo, diventato oggetto di un generale interesse scientifico per le importanti relazioni con la qualità e le caratteristiche nutrizionali e tecnologiche del latte. Il patrimonio caprino siciliano è rappresent…

Investigation of coat colour affecting genes in several sheep breeds

Preselection statistics and Random Forest classification identify population informative single nucleotide polymorphisms in cosmopolitan and autochthonous cattle breeds

Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and …

MOESM13 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 13: Figure S7. Genetic relationship defined with multidimensional scaling analysis between Italian and 62 European cattle breeds. The breeds were grouped according to their geographical origins and distributions. Northern_Europe (Belgian Blue, Dexter, Kerry, Lithuanian Light Grey, Lithuanian White Backed, Groningen Whitehead, Lakenvelder, Meuse-Rhine-Ijjsel, Norwegian Red, Finnish Ayrshire, Belted Galloway, Galloway, Angus, Scottish Highland, South Devon), England (Devon, Guernsey, Hereford, Longhorn, Lincoln Red, Milking Shorthorn, Red Poll, Beef Shorthorn, Sussex, Welsh Blach, White Park), Spain (Berrenda en Negro, Berrenda en Colorado, Cardena Andaluza, Menorquina, Pirena…

Development of multiplex-PCR protocol to amplify 12S and 16S rRNA genes of mtDNA for traceability of Sicilian mono-species dairy products.

Species identification in dairy sector is important not only to safeguard public health but also to verify compliance with the Production Regulations of many typical dairy products (PDO/PGI). The most common fraud in dairy sector is represented by the mixture of milks from different species, resulting in mislabeling of protected designation of origin (PDO) products. For a rapid, specific and sensitive identification of cattle’s, sheep’s and goat’s milk in mono-species Sicilian dairy products, species-specific multiplex-PCR protocol was developed. DNA from blood and experimental cheeses of Sicilian autochthonous breeds was used to amplify the 12S and 16S rRNA genes of the mitochondrial DNA. …

Selection signatures of fat tail in sheep

The investigation of the genes with a role in lipid metabolism enjoy considerable scientific and commercial interest because of the strong correlations between fat deposition and the risk of cardiovascular disease. The fat tail characteristic of sheep is the adaptive response to harsh environment, and beyond representing a valuable energy reserve for facing future climate changes provides clues for elucidating the physiology of fat deposition. Studies on various sheep populations detected fat-tail signatures on chromosomes 2, 3, 5, 6, 7 and 13. Fat-tailed sheep represent about 25% of the world’s sheep population, and the genes with a role in this phenotype are likely not the same for every …

MOESM6 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 6: Figure S3. Distribution of all ROH within breeds according to their size (kb).

A melanocortin 1 receptor (MC1R) gene polymorphism is useful for authentication of Massese sheep dairy products

Massese is an Italian sheep breed, with black or grey coat colour, mainly reared in the Tuscany and Emilia Romagna regions. Recently, the emerging interests in this breed have resulted in the production of Pecorino cheese obtained with only Massese milk. In order to be profitable, this marketing link between Massese breed and its products should be defended against fraudsters who could include milk of other sheep breeds or cow milk in Massese labelled productions. To identify the genetic factors affecting coat colour in sheep, we have recently analysed the melanocortin 1 receptor (MC1R) gene and identified several single nucleotide polymorphisms (SNPs). In this work, as a first step to set …

Genome-wide scan of fat-tail sheep identifies signals of selection for fat deposition and adaptation

Fat tail in sheep represents a valuable energy reserve for facing future climate changes. The identification of genes with a role in the fat-tail phenotype may contribute to understanding the physiology of fat deposition and the mechanisms of adaptation. Genotypic data obtained with the OvineSNP50K array in 13 thin-tail sheep breeds from Italy were used to identify selection signatures of fat tail through pairwise thin- versus fat-tail sheep breed comparisons, with the following fat-tail breeds of the Mediterranean area: two unique Italian fat-tail breeds (Barbaresca and Laticauda), a Barbary sheep breed from Libya, Ossimi breed from Egypt, Cyprus Fat-Tail and Chios from the Greek islands …

Genetic diversity and population structure of Sicilian sheep breeds using microsatellite markers

Abstract Genetic diversity studies in domestic animals aim at evaluating genetic variation within and across breeds mainly for conservation purposes. In Sicily, dairy sheep production represents an important resource for hilly and mountain areas economy. Their milk is used for the production of traditional raw milk cheeses, sometimes protected designation of origin (PDO) cheeses. In some cases, the quality of these products is linked to a specific breed, i.e. mono-breed labelled cheeses and it is therefore important to be able to distinguish the milk of a breed from that of others, in order to guarantee both the consumer and the breed itself. In order to investigate the genetic structure an…

Using of SNP markers to estimate inbreeding, coancestry and effective population size in Sicilian cattle breeds

Maintaining the highest levels of genetic diversity and limiting the increase in inbreeding is the premise of most conservation programs. The aim of this work was to estimate the inbreeding (F), coancestry (f) and effective population size (Ne) in two Sicilian cattle breeds, Cinisara (CIN) and Modicana (MOD). Rate of molecular inbreeding and coancestry were used to estimate the Ne. A total of 144 animals were genotyped using the Illumina Bovine SNP50K v2 BeadChip. The average molecular F and f coefficients were 0.68±0.024 and 0.67±0.03 in CIN and 0.69±0.020 and 0.70±0.03 in MOD cattle breeds, respectively. The results were not unexpected considering the reduced number of reared animals and …

Economic values for production and functional traits in Valle del Belice dairy sheep using profit functions

Abstract A deterministic static model was used to estimate the economic values (EV) of production (MY, milk yield; BW, birth weight; and ADG, average daily gain) and functional traits (ASR, adult survival rate; LSR, lamb survival rate; FE, fertility; PR, prolificacy; and LW ewe , mature weight of ewe) in Valle del Belice dairy sheep. In this study, values for the biological parameters and the production traits used in the model were taken from real data, by surveying 15 Valle del Belice farmers and reflected the production circumstances of pasture based dairy production systems. In this system feed cost accounted for 95% of total variable costs, whereas fixed costs were low and reflected tr…

Chromosomal assignment of the ovine hairless (hr) gene by fluorescence in situ hybridization.

Congenital hypotrichosis in mammalian species consists of partial or complete absence of a hair coat at birth. Affected individuals having a partial hair coat at birth may loose it subsequently.The aim of this paper was to physically map the ovine hr gene using fluorescence in situ hybridization (FISH).A preliminary study on an internet data bank (http://www.informatics.jax.org) showed that the regions of the hr gene on murine chromosome 14 and human chromosome 8 present homology with ovine chromosome 2.

Genome-wide association study reveals the locus responsible for microtia in Valle del Belice sheep breed.

Microtia is a congenital deformity of the outer ear with phenotypes varying from a small auricle to total absence (anotia). The genetic basis is still poorly understood, and very few studies have been performed in sheep. Valle del Belice sheep is a breed showing microtia. The aim of this study was to identify the potential genomic regions involved in microtia in sheep. A total of 40 individuals, 20 with microtia and 20 normal, were genotyped with the Illumina OvineSNP50 BeadChip. The comparison among the results from a genome-wide association study, Fisher's exact test and FST analysis revealed a single strong association signal: rs419889303 on chromosome 1, located within intron 3 of the C…

Development and validation of RP-HPLC method for the quantitative estimation of αs1-genetic variants in goat milk

A high-performance liquid chromatographic (HPLC) method was developed and validated for separation and quantification of the most common genetic variants of as1-casein in goat’s milk, to evaluate the effect of as1-casein polymorphisms on casein content. Chromatography was carried out by binary gradient technique on a reversed-phase C8 Zorbax column and the detection was made at a wavelength of 214 nm. The procedure was developed using individual raw milk samples of Girgentana goats. For calibration experiments, pure genetic variants were extracted from individual milk samples of animals with known genotypes, considering that commercial standards for goat genetic variants were not available.…

Studio dei rapporti di parentela tra individui della razza ovina Valle del Belice, mediante l’utilizzo di marcatori microsatelliti

Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

International audience; Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging to 23 sheep breeds of different geographic origins using the Rsb (extended haplotype homozygosity) and FST statistical approaches, to identify loci associated with the fat-tail phenotype. We also checked if these putative selection signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel signals and confirmed the presence of selection signature in genomic regio…

Analisi dei geni ASIP e MC1R in razze caprine con diversa colorazione del mantello

Development of an ad hoc natural whey starter culture for the production of Vastedda della valle del Belìce cheese

This work was aimed to characterize the autochthonous lactic acid bacteria (LAB) of PDO Vastedda della valle del Belìce cheeses, produced in several dairy factories, for the development of an ad hoc starter culture preparation for the production of this cheese. To this purpose, winter and spring productions were analysed, in order to isolate LAB adapted to perform the fermentation at low temperatures. Plate counts showed the total microbial counts (TMC) till levels of 9 -1almost 10 CFU g and all cheese samples were dominated by coccus LAB. Not all samples were positive for the presence of enterobacteria, but when they were found their concentrations were at similar levels in both seasons. A…

Initial allele frequencies for the prp gene of Valle del Belice pilot farms

MOESM2 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 2: Table S1. Name of the breeds, geographic coordinates (longitude and latitude) of the center of origin, sample size before (n-PreQC) and after (n-PostQC) genotyping quality control, and origin of genotyping data.

Sequence characterization of the melanocortin 1 receptor (MC1R) gene in sheep with different coat colour and identification of the putative e allele at the ovine Extension locus

Abstract Sequence of the melanocortin 1 receptor (MC1R) gene (the Extension locus) was obtained from a panel of 73 animals belonging to 9 Italian sheep breeds or populations (Appenninica, Bergamasca, Comisana, Cornigliese-like, Delle Langhe, Massese, Merinizzata Italiana, Sarda and Valle del Belice) with different coat colours. Evaluation of the identified polymorphisms on this phenotype was reported with in silico predictions and comparative approaches within and across breeds and across species. Five novel single nucleotide polymorphisms (SNPs), organized in three haplotypes, were detected. Another haplotype, including the two missense mutations already described for the ED allele, was id…

Genetic variability at αs2-casein gene in Girgentana dairy goat breed

Casein genes are highly polymorphic and the high degree of variability has qualitative and quantitative effects on milk composition thereby affecting chemical, physical and technological properties of goat milk. The aim of this work was to evaluate the genetic polymorphisms of the αs2-casein (CSN1S2) gene in the endangered Girgentana dairy goat breed in order to assess the genotypes distribution, as it is known genotype influences technological and nutritional milk properties. The study was performed on 207 sample of Girgentana goat breed, analysed with different PCR protocols. The most frequent alleles was A (0.722), followed by F (0.225), C (0.051) and E (0.002) while B, D and 0 alleles w…

APPLICATION OF SELECTED LACTIC ACID BACTERIA FOR THE YEAR-ROUND PRODUCTION OF VASTEDDALIKE CHEESE

Loss in milk yield and related composition changes resulting from different levels of somatic cell count in Valle del Belice dairy sheep

Mastitis is the most common and costly disease in the dairy industry and is responsible for several production effects. Mammary infections cause high somatic cell count (SCC) and severe damage to udder tissue and result in important losses of milk yield and quality, curd and cheese yields in dairy ewes. The aim of this study was to determine the effect of different levels of SCC on milk yield and composition in Valle del Belice dairy sheep. The original data set used for this study included 92,261 records of 6,763 ewes. Data were collected between 1994 and 2006 in 15 flocks. Test-day records of milk yield (MY), fat % (F%), protein % (P%), and SCC were collected following an A4 recording sch…

ANALYSIS OF MICROSATELLITE MARKERS IN SICILIAN GOATS BREED FOR TRACEABILITY OF GIRGENTANA TYPICAL DAIRY PRODUCTS

The establishment of useful analytical methods able to ensure the origin of the products, including the breed used, are important in maintaining the reliability of these products in order to develop a market segment. Traceability, obtained by molecular analysis, could be a reliable proposal for the authentication and valorization of animal products. In Sicily, the three most important dairy goat breeds are Girgentana (GR), Maltese (ML) and Derivata di Siria (DS). The GR is an endangered autochthonous goat breed. Preservation of endangered breeds could be achieved by establishing economic reasons for their survival. The aim of this work was to verify the use of microsatellite markers to asse…

Analysis of Illumina BovineSNP50 BeadChip data in different Italian cattle breeds to identify useful markers for breed authentication of dairy and beef products

The identification of the breed of origin of cattle derived products has recently assumed particular relevance since the increasing interest in marketing mono-breed labelled cheese and beef. These products are usually sold at a higher price creating financial incentives to substituting them with lower value products coming from undifferentiated or common breeds or crossbred animals. Frauds can damage these valuable niche markets that, indirectly, may help to preserve genetic diversity through the economic incentive on raising local breeds, derived by the high value products, that are usually less productive. DNA analysis can help to identify fraudulent behaviour as we already demonstrated f…

Additional file 11 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 11:PANTHER categories significantly overrepresented in goat CNVRs. PANTHER annotation has been obtained for the whole cattle genome. (DOC 101 KB)

Genetic characterisation of CSN2 gene in Girgentana goat breed

Among calcium sensitive caseins, β-casein is the most abundant in goat milk, representing up to 50% of total casein content. The goat β-casein locus has been widely investigated and at least ten alleles have been identified in different goat breeds. The aim of this work was to investigate the polymorphisms of β-casein gene in Girgentana dairy goat breed in order to assess the genotype distribution and evaluate how frequencies have changed during the last 10 years, as genotype is known to influence technological and nutritional milk properties. Sequencing analysis and alignment of the obtained sequences of β-casein exon 7, showed the presence of C, C1, and A strong alleles, and 0' null allel…

High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH h…

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

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.

A genomic map of climate adaptation in Mediterranean cattle breeds

International audience; Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate sub-types. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional…

Polymorphisms of β-defensin genes in Valle del Belice dairy sheep

The aim of this work was to study β-defensin 1 (SBD1) and β-defensin 2 (SBD2) genes in Valle del Belice dairy sheep in order to identify polymorphisms that can be utilized as markers of the analyzed genes, and search for the functional effects and roles of the identified polymorphisms (variation of the amino acid sequence of the protein and stability of mRNA molecule). The study was conducted on 300 randomly selected animals belonging to four flocks. A total of seven SNPs were identified, two in SBD1 and five in SBD2. The two SNPs identified in SBD2 coding region, at position 1659 and position 1667, were non-synonymous, leading to amino acid changes in the protein product. Nevertheless, the…

Effect of heat stress on production of Mediterranean dairy sheep.

A study on heat stress in Mediterranean dairy sheep was undertaken with the objective to examine the relationship between milk production and heat stress, to estimate the additive genetic variances of milk production traits and heat tolerance, and to investigate the possibility of future selection for increased heat tolerance. Production data included 59,661 test-day records belonging to 6624 lactations of 4428 lactating ewes from 17 flocks collected from 1994 through 2003. The traits investigated were daily milk yield, fat and protein percentage, and daily yield of fat-plus-protein. The pedigree file consisted of 5306 animals; in addition to the 4428 animals with records, 188 male and 690 …

Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat

Italy contains a large number of local goat populations, some of which do not have a recognized genetic structure. The “Mascaruna” is a goat population reared for milk production in Sicily. In this study, a total of 72 individuals were genotyped with the Illumina Goat_IGGC_65K_v2 BeadChip with the aim to characterize the genetic diversity, population structure and relatedness with another 31 Italian goat populations. The results displayed a moderate level of genetic variability for Mascaruna, in concordance with the estimated values for Italian goats. Runs of homozygosity islands are linked to genes involved in milk production, immune response and local adaptation. Population structure anal…

Missense and nonsense mutations in melanocortin 1 receptor (MC1R) gene of different goat breeds: association with red and black coat colour phenotypes but with unexpected evidences

Abstract Background Agouti and Extension loci control the relative amount of eumelanin and pheomelanin production in melanocytes that, in turn, affects pigmentation of skin and hair. The Extension locus encodes the melanocortin 1 receptor (MC1R) whose permanent activation, caused by functional mutations, results in black coat colour, whereas other inactivating mutations cause red coat colour in different mammals. Results The whole coding region of the MC1R gene was sequenced in goats of six different breeds showing different coat colours (Girgentana, white cream with usually small red spots in the face; Maltese, white with black cheeks and ears; Derivata di Siria, solid red; Murciano-Granad…

Two-dimensional difference in gel electrophoresis (2D-DIGE) for milk proteins characherization in Girgentana goat breed

Milk proteomics has rapidly become an eligible approach, since the protein fraction constitutes the most biologically relevant component in milk. Proteomic applications can vary greatly from straightforward protein identification to complex characterization of post-translational modifications and protein-protein interactions. The aim of this work was to compare protein profile of Girgentana whole milk samples between lactation periods and geographical areas by two dimensional difference in gel electrophoresis (2D-DIGE). Milk samples were collected in two flocks located in two different areas of Sicily at three different time points from calving: 30, 55, and 120 days, respectively. Protein p…

Parentage verification of Valle del Belice dairy sheep using microsatellite markers

The objectives of the present work were to evaluate polymorphism of microsatellite markers, develop a parentage test and estimate misidentification rate on Valle del Belice Sicilian dairy sheep breed. Polymorphism was evaluated from 184 randomly selected animals from 5 different flocks. A total of 21 microsatellite markers including CSRD247, ILST011, McM527, APO010, INRA132, DU194351, DU323541, FCB128, McM16, OarCP49, ILST087, DU223896, ILST005, TCRVB06, SPS113A, INRA063A, SPS115, DU206192, DU216028, BM827 and McM54 were amplified using three PCR reactions and fragment lengths determined in a single multiplex electrophoresis run. Markers were easily genotyped, very polymorphic and in Hardy-…

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data. Moreover, the breed's genetic structure and its relationship with oth…

Determination of milk production losses and variations of fat and protein percentages according to different levels of somatic cell count in Valle del Belice dairy sheep

The somatic cell count (SCC) of milk is widely used to monitor udder health and the milk quality and because of its positive genetic correlation with mastitis this trait was included in breeding schemes of dairy sheep. The aim of this study was to estimate the loss in milk yield (MY) and related composition resulting from different levels of somatic cell count in Valle del Belice dairy sheep. Data were collected between 2006 and 2016 in 15 flocks following an A4 recording scheme. Somatic cell count (SCC), fat and protein percentage (F% and P%) were determined using mid-infrared spectroscopy. To evaluate loss in test day MY, F% and P%, five different classes of SCC were arbitrarily defined: …

MOESM3 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 3: Figure S1. Trends in historic effective population size (Ne) (from 13 to 98 generations).

Genome-wide assessment of diversity and differentiation between original and modern Brown cattle populations

Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity (ROH) islands using the Illumina Bovine SNP50 BeadChip genotyping data. After quality control, 34 735 SNPs and 106 animals were retained for the analyses. Larger heterogeneity was highlighted for the original populations. Patterns of genetic differentiation, multidimensional scaling, and the neig…

Genetic and environmental sources of variation for milk yield traits in Barbaresca siciliana breed

Abstract Multi-trait animal model procedures were used to calculate variance for milk yield traits in the Barbaresca siciliana breed. The recorded data consisted of 14 791 lactations from 6678 ewes distributed among 44 herds from six provinces in Italy. The data-set with pedigree information used for the estimation of genetic parameters and correlation, included 6678 ewes with records, 757 dams, 4 paternal grandams, 28 maternal grandam and 2 maternal great-grandams, all without records, and additionally 301 sires, 3 paternal grandsires, 11 maternal grandsires and 1 maternal great-grandsires. The variables considered in the present study were the milk yield at 100 days (MY-100), 120 days (MY…

Population genetic structure and milk production traits in Girgentana goat breed

The aim of this work was to evaluate the genetic status of the Girgentana goat, an endangered breed from Sicily (Italy), using microsatellite markers. Furthermore, as the main purpose of the Girgentana breed is milk production, quantitative milk traits were investigated, including fatty acid profile. Molecular data from CSN1S1, CSN2, CSN1S2, and CSN3 casein genes were also used to infer haplotypes. A total of 264 individuals were collected. Samples of Maltese (n = 41) and Derivata di Siria (n = 33) goat breeds were also used to understand the genetic relationship among breeds. Test-day records for milk production were collected to determine daily milk yield, fat, protein, casein, lactose, a…

QUANTIFICATION OF GENETIC VARIANTS OF CASEINS IN MILK OF GIRGENTANA GOAT BREED

In the milk of ruminants, more than 95% of proteins are synthesized by six structural genes, four caseins (alphas1, beta, alphas2 and κ-caseins) and two whey proteins (alpha-lactalbumin and beta-lactoglobulin). Goat casein genes have been found to show high polymorphism, which influences not only the quantity of casein in milk but also the structural and nutritional characteristics and technological properties of milk. The aim of this work was to separate and quantify the most common allelic variants of caseins in milk of Girgentana goat breed, a Sicilian autochthonous breed, and to evaluate the effect of casein polymorphisms on casein content. The alleles at different casein genes were det…

Additional file 10 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 10: Figure S8. Projection on a single LDA axis in the model-grouping approach (a) and on the first two LDA axes in the six scenarios separately (b).

Copy number variation and missense mutations in the caprine agouti signaling protein (ASIP) gene are present in goat breeds with different coat colour

Identification, typing, and investigation of the dairy characteristics of lactic acid bacteria isolated from 'Vastedda della valle del Belìce' cheese

Traditional cheeses made without starter cultures can be characterised by the attribute of instability. The addition of autochthonous starter cultures can ensure stability without compromising the characteristics of the final product. This study aimed to characterise the autochthonous lactic acid bacteria (LAB) population in “Vastedda della valle del Belice” cheeses, which have a protected designation of origin (PDO) status, in order to develop an ad hoc starter culture to be used in its future production. Winter and spring productions were analysed to ensure isolation of specific LAB that had adapted to perform fermentation at low temperatures. Plate counts revealed total microbial numbers…

MOESM1 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 1. Description of each Italian local cattle breed involved in this study [68].

Haplotypes of Single Nucleotide Polymorphisms (SNPs) in casein loci of Girgentana goats explain isoelectrofocusing results.

Goat milk, cheese and yoghurt offer an alternative to cow milk products. In Sicily one of the important goat breeds reared is the Girgentana. Traditionally the milk from Girgentana goats was used for nourishment of infants and elderly. Recently, the Girgentana breed has been in decline. This of concern, as the Girgentana may carry unique milk protein genetic variants. If health benefits of Girgentana goat milk is proven, then increasing production from this population will be of great interest. The most abundant proteins in goat milk, as in other milks, are the caseins, αS1-, β-, αS2- and κ-casein, coded by the loci CSN1S1, CSN2, CSN1S2 and CSN3 respectively. In other goat breeds, the casei…

Effect of somatic cell count on longevity in dairy ewes using survival analysis

Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

Background Because very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F$$\end{document}F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from t…

Microbial Activation of Wooden Vats Used for Traditional Cheese Production and Evolution of Neoformed Biofilms.

ABSTRACT Three Lactococcus lactis subsp. cremoris strains were used to develop ad hoc biofilms on the surfaces of virgin wooden vats used for cheese production. Two vats (TZ) were tested under controlled conditions (pilot plant), and two vats (TA) were tested under uncontrolled conditions (industrial plant). In each plant, one vat (TA1 and TZ1) was used for the control, traditional production of PDO Vastedda della Valle del Belìce (Vastedda) cheese, and one (TA2 and TZ2) was used for experimental production performed after lactococcal biofilm activation and the daily addition of a natural whey starter culture (NWSC). Microbiological and scanning electron microscopy analyses showed differenc…

Risk assessment of selection for restistant PrP alleles on milk production in Valle del Belice

Effect of heat stress on production in Mediterranean dairy sheep

Identificazione di una nuova variante alla κ-caseina nella razza caprina Girgentana

La κ-caseina è la lattoproteina che determina la grandezza e la funzione specifica delle micelle nel latte e la sua idrolisi, chimosina dipendente, è responsabile della coagulazione del latte stesso. Il gene della κ-caseina comprende 5 esoni. Ad oggi sono state identificate 16 varianti alleliche, di cui 13 sono varianti proteiche e 3 mutazioni silenti, per un totale di 15 siti polimorfici.Lo scopo di questo lavoro è stato la caratterizzazione dell’esone 4 del gene della κ-caseina nella razza caprina Girgentana. Un nuova variante alleliche, denominata X, è stata riscontrata con una frequenza relativamente bassa (0,04).

Test-Day Model Heritabilities for somatic cvell score and production traits in primiparous Valle del Belice sheep

A repeatability test-day animal model was used to investigate heritabilities of somatic cell score (SCS) and milk production traits in Valle del Belice sheep. The heritability estimate for SCS falls within the range reported in literature (0.14±0.03), while estimates for milk production and composition traits were below those obtained by others, 0.12±0.03, 0.09±0.02, 0.14±0.03, 0.14±0.03, and 0.12±0.03, respectively, for milk yield, fat %, fat yield, protein %, and protein yield. Flock-test-day had a substantial effect on milk production traits but not on SCS. These results provide the basic parameters required for discussion of selection strategies and objectives in Valle del Belice sheep.

Caratterizzazione genetica mediante microsatelliti di una popolazione caprina siciliana

I microsatelliti sono ad oggi i marcatori molecolari maggiormente utilizzati per la caratterizzazione genetica nei caprini. Lo scopo del presente lavoro è stato quello di caratterizzare la struttura genetica della capra Mascaruna per verificare se può essere definita come una popolazione. L’analisi è stata condotta utilizzando un pannello di 18 microsatelliti. Il DNA è stato estratto da 60 individui di cui 20 Mascaruna (MAS), 20 Girgentana (GIR) e 20 animali derivanti da diversi incroci (MIX). Un totale di 148 alleli sono stati osservati di cui 106 in GIR, 107 in MAS e 129 in MIX; il valore del PIC è di 0,69 e tutti i marcatori hanno mostrato un numero di alleli superiori a 4. Valori più al…

LINKAGE DISEQUILIBRIUM AND GENETIC DIVERSITY IN TWO SICILIAN CATTLE BREEDS ASSESSED BY BOVINE SNP CHIP

The Modicana (MOD) and Cinisara (CIN) are two Sicilian cattle breeds farmed in extensive systems and their economic importance lies on the traditional making of two typical ‘pasta filata’ cheeses. The aim of this study was to explore the genetic structure and the extent of Linkage Disequilibrium (LD) of MOD and CIN cattle breeds. A total of 144 animals were genotyped, using the Bovine SNP50K v2 BeadChip. The squared correlation coefficient between two loci (r2) was used as a measure of LD. Principal components analysis (PCA), molecular inbreeding (F) and Bayesian clustering algorithm (Pritchard et al., 2000) were used to explore the relationship between individuals and populations. The r2 r…

Valorization of indigenous dairy cattle breed through salami production

The aim of the research was to produce salami manufactured with meat of three different commercial categories of bovine breed: cow on retirement, beef and young bull. A total of six experimental productions, at small-scale plant, were carried out with and without starter culture inoculums. The evolution of physico-chemical parameters in all trials followed the trend already registered for other fermented meat products. Several LAB species were found during process with different levels of species diversity and frequency of isolation among inoculated (mainly Pediococcus pentosaceus and Staphylococcus xylosus) and uninoculated (mainly Enterococcus devriesei, Lactobacillus curvatus and Lactoba…

Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations.

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments &gt

Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep.

Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 C…

Effect of somatic cell count level on functional longevity in Valle del Belice dairy sheep assessed using survival analysis.

The objectives of this study were to evaluate the effect of somatic cell count (SCC) on functional longevity and to estimate the heritability of functional longevity using survival analysis in Valle del Belice dairy sheep. A total of 4,880 lactations of 2,190 ewes from 11 flocks were used. In this study, SCC was considered as an indication of subclinical mastitis. In case of clinical cases, identified by the technicians at milking time, test-day weights and milk samples of those ewes were not considered. Somatic cells were analyzed as counts, without any transformation, and were grouped in 3 classes based on the observed SCC maximum (mxSCC). The mxSCC classes, expressed as 103 cells/mL, wer…

Effect of weather conditions on somatic cell score in Sicilian Valle del Belice ewes

Mastitis susceptibility of Valle del Belice ewes from the south of Sicily to temperature, humidity, precipitation, solar radiation, sun hours, air pressure, wind-speed and wind-direction measured by a public weather station was investigated using 65,848 test-day somatic cell score (SCS) records of 5,237 ewes. All weather parameters had an effect on SCS in a regression approach. Extreme values of maximum and minimum temperaturehumidity indices resulted in increased SCS. Higher precipitation, solar radiation and sun hours resulted in increased SCS, whereas higher air pressure and wind speed resulted in reduced SCS.

Genome-wide association studies for milk production traits in Valle del Belice sheep using repeated measures

Genome-wide association studies (GWASes) have become a powerful tool for identifying genomic regions associated with important traits in livestock. Milk production traits in dairy sheep are measured at different time points during their life span. Using phenotypic data generated from longitudinal traits could improve the power of association studies but until now have received less attention in GWASes as a methodology and has not been implemented. The aim of this study was to carry out a GWAS for milk production traits in Valle del Belice sheep using repeated measures. After quality control, 469 ewes and 37 228 SNPs were retained for the analysis, and phenotypic data included 5586 test-day …

Identification of two new alleles at k-casein (CSN3) gene in Girgetana goat breed

In the milk of ruminants, more than 95% of proteins are synthesized by six structural genes, four caseins and two whey proteins. The κ-casein fraction plays an important role in the formation, stabilization and aggregation on casein micelles and thus affects technological and nutritional properties of milk. Goat κ-casein (CSN3) gene comprises five exons with the mRNA coding region for mature protein spanning from exon 3 to exon 4. The κ-casein locus has been widely investigated and several genetic variants have been found in different goat breeds. At protein level, AIEF and BIEF groups corresponding to isoelectric point 5.53 and 5.78, respectively, have been identified. In this study, exon …

Genetic selection for reduced Somatic Cell Counts in sheep milk: A review

Mastitis is an inflammation of the udder, mainly caused by bacteria, and leads to economic loss, due to discarded milk, reduced milk production, reduced milk quality and increased health costs in both dairy sheep and cattle. Selecting for increased genetic resistance to mastitis can be done directly or indirectly, with the indirect selection corresponding to a prediction of the bacteriological status of the udder based on traits related to the infection. The most frequently used indirect method is currently milk somatic cell count (SCC) or somatic cell score (SCS). This review reports the state of the art relating to the genetic basis of mastitis resistance in sheep and explores the opportu…

Mutations of the MC1R gene in Sicilian goat breeds, relationships with coat colours and perspectives for their use in breed traceability systems of goat products

Parentage assignement-its relationships with heterozigosity and molecular coancestry

PRELIMINARY STUDY ON QUANTIFICATION OF aS1-CASEIN VARIANTS IN GIRGENTANA GOAT BREED BY DIRECT CHROMATOGRAPHIC ANALYSIS OF MILK

Goat αs1-casein is a highly polymorphic protein, coded by CSN1S1 gene. Nowadays, several alleles were identified and associated with different levels of αs1-casein in goat milk. Polymorphisms at αs1-casein locus have been shown to affect not only the quantity of this casein in goat milk, but also the structural and nutritional characteristics (hypoallergenic properties) and technological properties of the milk (1). The aim of this work was to separate and quantify the most common allelic variants of αs1-casein in milk of Girgentana goat breed, a Sicilian autochthonous breed, and to evaluate the effect of αs1-casein polymorphisms on casein content. The CSN1S1 A/01, B/E, F, and N alleles were…

Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability

Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aega…

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

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&rsquo

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…

Polymorphisms of beta-lactoglobulin promoter region in three Sicilian goat breeds

Several beta-lactoglobulin (BLG) polymorphisms have been described within the proximal promoter region and coding region of the caprine gene, although no genetic variants affecting the protein amino acid composition and/or expression level have been characterized so far. Binding sites for several transcription factors (TFs) are present in the BLG promoter region. The aims of this work were to sequence the full-length promoter region of three Sicilian goat breeds in order to identify polymorphisms, analyze the identified haplotypes, search for differences between breeds for the presence of polymorphisms in this gene region, search for putative TFs binding sites, and check if polymorphisms la…

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

Simple Summary The aim of this work is to identify CNVs and perform a CNV-based population genetics analysis in five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs and 365 CNV regions (CNVRs). The different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups. Gene enrichment was described for the 37 CNVRs selected considering the top 10%. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. CNVs represent valuable molecular resources to provide useful information for separating the p…

ASSOCIATION BETWEEN THE POLYMORPHISM AT CASEIN LOCI AND MILK FATTY ACID COMPOSITION IN GIRGENTANA GOATS

composition is an important trait for the goat dairy industry because of its influence on cheese yield and the organoleptic properties of dairy products (Chilliard et al., 2003). Goat milk is particularly rich in saturated fatty acids (SFA) whereas monounsaturated (MUFA) and polyunsaturated (PUFA) FA are less abundant (Fontecha et al., 2000).The aim of this work was to provide new data to better understand the influence of polymorphism at casein loci on fatty acid profile in Girgentana goat milk. One hundred lactating Girgentana goats, homogeneous for milk production, days of lactation, body weight and diet were used. The procedure was developed using individual raw milk samples, collected …

Genetic characterization of the Mascaruna goat, a Sicilian autochthonous population, using molecular markers

The aim of this work was to characterize a Sicilian autochthonous goat population using microsatellite markers and genetic polymorphisms at the casein genes. In order to investigate the genetic structure of the Mascaruna goat, a total of 60 (20 Girgentana, 20 mixed populations, and 20 Mascaruna) individuals were analyzed, using a panel of 18 microsatellite markers. Moreover, the Mascaruna goats were genotyped at casein loci using several molecular techniques. Based on the genetic structure at casein genes, the Mascaruna goat was similar to most goat breeds from the Mediterranean area, which are characterized by the predominance of strong alleles. The low value of genetic differentiation amo…

Use of microsatellite markers for genetic traceability of Girgentana dairy products

Genetic traceability is based on the identification of both animals and their products through the study of DNA. With the goal of developing a genetic traceability system for dairy products, the aim of this study was to identify specific microsatellite markers able to discriminate among the most important Sicilian dairy goat breeds, in order to detect possible adulteration in Girgentana dairy products. A total of 20 microsatellite markers were analyzed on a total of 338 individual samples from Girgentana (GIR), Maltese (MAL) and Derivate di Siria (DdS) goat breeds. The first step was to identify breed specific microsatellite markers that can be used for the traceability of dairy products. A…

A pipeline for variants discovery using next-generation DNA sequencing data

Recent advances in next generation sequencing (NGS) technology provide a cost-effective approach to large-scale resequencing of livestock samples in order to study several biological phenomena. NGS produces millions of short DNA sequences that require an unbiased way to make possible comprehensive searches for variation to identify putative causative mutations for economically important traits. The aim of this work was to present a bioinformatics pipeline analysis for variants discovery in ovine genome. A total of 30 individuals belonging to Valle del Belice dairy ewes was used for whole genome sequencing of pooled libraries prepared using Illumina Nextera Kit. Paired-end sequencing was car…

Genome structure in Sicilian cattle breeds

Genomic technologies provide background information concerning genome structure in domestic animals. The aim of this work was to investigate the genetic structure and the patterns of linkage disequilibrium (LD) in two Sicilian local cattle breeds, Cinisara and Modicana. Genotypes from animals of Italian Holstein breed were also used to investigate the relationship among breeds. Structure software was used to analyze the genetic structure and assign the individuals to each cluster. The genetic relationship between individuals was estimated by Principal Components Analysis (PCA) of genetic distance. A standard descriptive LD parameter (r2) was obtained between adjacent SNPs and for all pairwi…

Genome-wide detection of copy-number variations in local cattle breeds

The aim of the present study was to identify copy-number variations (CNVs) in Cinisara (CIN) and Modicana (MOD) cattle breeds on the basis of signal intensity (logR ratio) and B allele frequency of each marker, using Illumina’s BovineSNP50K Genotyping BeadChip. The CNVs were detected with the PennCNV and SVS 8.7.0 software and were aggregated into CNV regions (CNVRs). PennCNV identified 487 CNVs in CIN that aggregated into 86 CNVRs, and 424 CNVs in MOD that aggregated into 81 CNVRs. SVS identified a total of 207 CNVs in CIN that aggregated into 39 CNVRs, and 181 CNVs in MOD that aggregated into 41 CNVRs. The CNVRs identified with the two softwares contained 29 common CNVRs in CIN and 17 co…

Estimation of genetic and phenotypic parameters for bacteriological status of the udder,somatic cell score,and milk yield in dairy sheep using a threshold animal model

Abstract The objective of this study was to estimate the genetic parameters for infection status (INF), as indicator of mastitis, SCS (i.e., log-transformed SCC), and milk yield (MY), by using a Gibbs sampling algorithm. The data comprised 17,843 test-day records of 2040 ewes. The pedigree file included 2948 animals. A bivariate variance component analysis was performed using the TM software. Fixed effects considered in the analysis were litter size, parity, flock by test-day interaction, year by season of lambing interaction, and stage of lactation; whereas the animal, and the permanent environmental effect within and across lactations were considered as random as well as the error. Flat p…

La capra Messinese

Ecologia delle popolazioni lattiche associate alle farine di frumento e studio delle attitudini tecnologiche per la produzione di impasti acidi

Il presente lavoro ha previsto inizialmente l’isolamento, la tipizzazione e l’identificazione dei batteri lattici (BL) presenti in campioni di farine utilizzate per prodotti da forno a lievitazione naturale prelevati presso diversi panifici siciliani. Le conte in piastra dei BL sono state ottenute su tre differenti terreni colturali, generici e specifici. I risultati hanno evidenziato una concentrazione massima di BL di 4.75 Log UFC/g. Tutte le colonie diverse sono state isolate e purificate. Le colture sono state differenziate sulla base delle caratteristiche fenotipiche e dei profili generati mediante la tecnica randomly amplified polymorphic DNA (RAPD)-PCR che ha permesso il riconoscimen…

Parentage verification of Valle del Belice dairy sheep using multiplex microsatellite panel

Abstract The aim of this work was to develop and evaluate a PCR based microsatellite markers multiplex system for parentage verification of Sicilian Valle del Belice dairy sheep. A total of 85 samples of blood and hair were collected and genotyped for 24 microsatellite markers in multiplex electrophoresis runs. A total of 269 alleles were detected across the 24 loci investigated. The PIC considering all loci was equal to 0.736, showing that this microsatellite panel was very polymorphic and highly informative. A parentage test was performed on 64 families generated with multiple sires. Results indicated 20.3% and 29.7% misidentification rates for females and males, respectively. In 8 cases,…

Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds.

The effects of inbreeding in livestock species breeds have been well documented and they have a negative impact on profitability. The objective of this study was to evaluate the levels of inbreeding in Sarda (SAR, n = 785) and Valle del Belice (VdB, n = 473) dairy sheep breeds and their impact on milk production traits. Two inbreeding coefficients (F) were estimated: using pedigree (FPED), or runs of homozygosity (ROH; FROH) at different minimum ROH lengths and different ROH classes. After the quality control, 38,779 single nucleotide polymorphisms remained for further analyses. A mixed-linear model was used to evaluate the impact of inbreeding coefficients on production traits within each …

Receiver-operating characteristic curves for somatic cell scores and California mastitis test in Valle del Belice dairy sheep.

Using receiver-operating characteristic (ROC) curve methodology this study was designed to assess the diagnostic effectiveness of somatic cell count (SCC) and the California mastitis test (CMT) in Valle del Belice sheep, and to propose and evaluate threshold values for those tests that would optimally discriminate between healthy and infected udders. Milk samples (n = 1357) were collected from 684 sheep in four flocks. The prevalence of infection, as determined by positive bacterial culture was 0.36, 87.7% of which were minor and 12.3% major pathogens. Of the culture negative samples, 83.7% had an SCC < 500,000/mL and 97.4% had <1,000,000 cells/mL. When the associations between SC score (SC…

Cellule somatiche ed isolamento di agenti mastidogeni in ovini di razza Valle del Belice

Il conteggio delle cellule somatiche nel latte ovino si è dimostrato un valido strumento per la determinazione dello stato sanitario della mammella. Oggetto del presente studio è stato valutare eventuali relazioni fra il contenuto in cellule somatiche (SCC) e le infezioni mammarie (IMI) negli ovini. L’indagine è stata condotta nel periodo 2006-2012 su n.14072 campioni di latte individuale. In base al tenore i campioni sono state inseriti in 4 classi: 300.000; da 301.000 a 500.000; da 501.000 a 1.000.000 e ≥1.001.000 cellule/ml. Per l’isolamento colturale sono stati seminati 10 μl di latte su piastre di Agar Sangue incubate per 24-48 h a 37 °C in aerofilia e, se necessario, in microaerof…

MOESM10 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 10: Figure S6. Scatter plot of correlations between genetic differentiation (FST) and geographical distances for all breeds.

La Messinese risorsa autoctona tutta siciliana

Scopo del presente lavoro è la presentazione della situazione attuale e delle prospettive future di sviluppo e valorizzazione della capra Messinese, che tra le popolazioni autoctone siciliane, presenta buone caratteristiche produttive. La capra Messinese è largamente diffusa nella zone dei monti Nebrodi dove prevale l’allevamento brado. Il fabbisogno alimentare è dato da pascoli naturali con integrazione di fave e fieno polifita. La mungitura è manuale. La stagione di monta ha inizio a giugno quando i becchi vengono immessi nelle greggi. Dal punto di vista fenotipico, gli individui mostrano un mantello che nella maggior parte dei casi è nero ma può anche presentarsi grigio, marrone e rossic…

Effect of the PRP gene on milk production in Valle del belice sheep

Demographic characterization and genetic variability of the Girgentana goat breed by the analysis of genealogical data

The aim of this paper is to present an overview of the actual Sicilian Girgentana population structure by the analysis ofgenealogical data. Statistics show that in 1983 the population consisted of 30,000 Girgentana goats; ten years lateralmost 98% of the entire Girgentana population disappeared. The remaining population consists of 461 individuals (134males and 327 females), with 368 living animals. The effective population size is 380 individuals. The inbreeding rate pergeneration was equal to 0.13%. The average estimated inbreeding level within the living male population was equal to0.8% (0-15%); and the average inbreeding level within the living female population was equal to 0.7% (0-31%…

On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

AbstractBackgroundDuring the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, throug…

Genetic variability of Girgentana goat breed using molecular markers

Assessing genetic diversity of local breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. The aim of this work was to quantify the levels of genetic variability in Girgentana goat breed using microsatellite markers and genetic polymorphisms at the casein genes. A total of 264 individuals were genotyped for 20 microsatellites, selected as suggested by ISAG and FAO. Moreover, the same individuals were characterized for the casein loci (CSN1S1, CSN2, CSN1S2, and CSN3) using PCR and sequencing protocols. Several genetic diversity indexes were estimated. A total of 130 a…

Additional file 10 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 10:Gene ontology (GO) categories significantly overrepresented in goat CNVRs at different False Discovery Rate (FDR) levels. GO categories were Molecular function, Biological process, and Cellular component. (DOC 118 KB)

Comparison of PrP allele frequencies of non-infected Valle del Belice and infected cross-breed dairy sheep flocks

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

Abstract 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 polymorphi…

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…

Additional file 3 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 3: Table S2. Set of priors used to model the scenarios in the ABC framework.

Analysis of the influence of the PrP genotype on the litter size in Polish sheep using classification trees and logistic regression

The relation between prion protein (PrP) genotype class and litter size was analysed in Polish Merino, Black-headed, Ile de France and Berrichon du Cher sheep in Poland. Litter size was analysed with the classification tree technique and multiple logistic regression for effects of breed, age of ewe, PrP genotype, litter size of ewe at her birth, and at her rearing and year of ewe's birth. The resulting classification tree was 6-level deep and contained 21 leaves. Age, breed and year of birth were more important determinants of litter size than PrP genotype. Importance of PrP genotype in the tree development was 0.560 relative to age of ewe. While the logistic regression analysis showed that…

MOESM4 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 4: Table S2. Pearson correlation coefficients between genetic diversity indices. Observed (Ho) and expected (He) heterozygosity, average minor allele frequency (MAF), inbreeding coefficient (FHOM), contemporary effective population size (cNe), mean ROH-based inbreeding coefficient (FROH&gt;4Mb) and recent and historical Ne estimated 13 (Ne13), 20 (Ne_20 and 80 (Ne_80) generations ago. (* p- valueâ

Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping

The aim of this study was to identify genomic regions underlying milk production traits in the Valle del Belice dairy sheep using regional heritability mapping (RHM). Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY), collected over a period of six years (2006-2012) on 481 Valle del Belice ewes, were used for the analysis. Animals were genotyped with the Illumina 50k SNP chip. Variance components, heritabilities, and repeatability within and across lactations were estimated, fitting parity, litter size, season of lambing, and fortnights in milk, as fixed; and additive genetic, permanent environment within and across …

Demographic, Genealogical and morphological characterization of Pantelleria donkey

A demographic, genetic and morphologi­cal evaluation on Pantelleria donkey's population was carried out to give a con­tribution for the exploitation of this old donkey breed. Genealogical data were analysed by the software Minbreed v 1.0. Pedigree is com­posed by 4 generations. The inbreeding of the population (Fwhole population = 0.4 %) resulted very low than the expectations; therefore, the inbreeding coefficients resul­ted low in the males F male, = 0.9 % and in the females Ffemale = 0.0 %. On the other hand, the mean relationship among the 378 couplings resulted very high a1j = 15,1 %. The morphological study was carried out on 20 subjects. For each animal the most important morphologic…

Weighted Single-Step Genome-Wide Association Study Uncovers Known and Novel Candidate Genomic Regions for Milk Production Traits and Somatic Cell Score in Valle del Belice Dairy Sheep

The objective of this study was to uncover genomic regions explaining a substantial proportion of the genetic variance in milk production traits and somatic cell score in a Valle del Belice dairy sheep. Weighted single-step genome-wide association studies (WssGWAS) were conducted for milk yield (MY), fat yield (FY), fat percentage (FAT%), protein yield (PY), protein percentage (PROT%), and somatic cell score (SCS). In addition, our aim was also to identify candidate genes within genomic regions that explained the highest proportions of genetic variance. Overall, the full pedigree consists of 5534 animals, of which 1813 ewes had milk data (15,008 records), and 481 ewes were genotyped with a …

MOESM7 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 7: Figure S4. Model-based clustering of the estimated membership fractions of individuals from the 32 breeds analyzed in each of the K inferred clusters revealed by the ADMIXTURE software (Kâ =â 12, 16, 20, 28, 32). For a full definition of breeds see Table S1 (see Additional file 2: Table S1).

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

Genomic technologies, such as high- throughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to inves- tigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (N e ), and the patterns of linkage disequilibrium (LD) in 2 eco- nomically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. To understand the genetic rela- tionship and to place both Sicilian breeds in a global context, genotypes from 134 other domesticated bovid breeds were used. Principal component analysis showed that…

Genome-wide analyses reveal the regions involved in the phenotypic diversity in Sicilian pigs.

Nero Siciliano (Sicilian Black, SB) is a local pig breed generally of uniform black color. In addition to this officially recognized breed, there are animals showing morphological characteristics resembling the SB but with gray hair (Sicilian Grey, SG). The SG, compared with the SB, also shows a more compact structure with greater transverse diameters, higher average daily gains and lower thickness of the back fat. In this study, using the Illumina PorcineSNP60 BeadChip, we run genome-wide analyses to identify regions that may explain the phenotypic differences between SB (n = 21) and SG (n = 27) individuals. Combining the results of the two case–control approaches (GWAS and FST), we identi…

β-lactoglobulin gene promoter: new SNPs in sheep and goat

β-lactoglobulin (β-lg) is the major whey protein in milk of ruminants and several non ruminant species, but it is lacking in rodents, lagomorphs and human. The aim of this work was sequencing the promoter region of β-lg gene in Sicilian sheep and goat dairy breeds, in order to identify polymorphisms. In these species, the promoter region was aligned using the sequences available on database. A common set of primers was designed to amplify and sequence a fragment of approximately 2.1 kb. Within this region, 12 single nucleotide polymorphisms (SNPs) were identified in goat breeds: 7 out of them were not yet reported in literature. Moreover, in sheep breeds 15 SNPs were newly identified. Using…

Effects of different simplified milk recording methods on genetic evaluation with Test-Day animal model

The aims of the present study were to compare estimated breeding values (EBV) for milk yield using different testing schemes with a test-day animal model and to evaluate the effect of different testing schemes on the ranking of top sheep. Alternative recording schemes that use less information than that currently obtained with a monthly test-day schedule were employed to estimate breeding values. A random regression animal mixed model that used a spline function of days in milk was fitted. EBVs obtained with alternative recording schemes showed different degrees of Spearman correlation with EBVs obtained using the monthly recording scheme. These correlations ranged from 0.77 to 0.92. A redu…

Variation of proteomic profile during lactation in Girgentana goat milk: a preliminary study

The knowledge of milk proteome has been greatly enhanced by technological advances in the proteomics field as the use of the two-dimensional differential in-gel electrophoresis, a gel-based approach which allowed the analysis of proteins from complex mixtures and the comparing of several protein samples in the same experiment. The aim of this study was to characterise the whole milk proteomic profile in Girgentana dairy goat breed by two-dimensional differential in-gel elecrophoresis. The obtained representative 2D whole milk proteomic map showed a general picture of the protein distributions over the pH 3–10 NL including about 100 spots, most of them organised like a spot train. Among diff…

Full-length sequencing and identification of novel polymorphisms in the ACACA gene of Valle del Belice sheep breed

The essential role of the acetyl-CoA carboxylase (ACACA) enzyme in milk fatty acid (FA) synthesis suggests that it may be responsible for the phenotypic variability observed in milk. Before attempting association analyses between this gene and/or enzyme and phenotypic traits, a study on the genetic variability within this locus is required. The aim of this work was to sequence the entire coding region of ACACA gene in Valle del Belice sheep breed to identify polymorphic sites. A total of 51 coding exons of ACACA gene were sequenced in 32 individuals of Valle del Belice sheep breed. Sequencing analysis and alignment of obtained sequences showed the presence of 23 polymorphic sites. The most …

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

In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient (F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs 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 F derived from ROH (F-ROH) in three local dairy cattle breeds. F-ROH values were compared with F estimated from the genomic relati…

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

Application of microsatellite markers as potential tools for traceability of Girgentana goat breed dairy products

In livestock, breed assignment may play a key role in the certification of products linked to specific breeds. Traceability of farm animals and authentication of their products can contribute to improve breed profitability and sustainability of animal productions with significant impact on the rural economy of particular geographic areas and on breed and biodiversity conservation. With the goal of developing a breed genetic traceability system for Girgentana dairy products, the aim of this study was to identify specific microsatellite markers able to discriminate among the most important Sicilian dairy goat breeds, in order to detect possible adulteration in Girgentana dairy products. A tot…

Additional file 4 of The genetic heritage of Alpine local cattle breeds using genomic SNP data

Additional file 4: Table S2. Fixation indices (FST) between all pairs of breed populations analyzed in this study.

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations.

Selective breeding has led to modifications in the genome of many livestock breeds. In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case–control genome-wide association study (GWAS), the Bayesian population differentiation analysis (FST) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and FST and one marker bet…

Genome-wide association study for milk production traits in Valle del Belice sheep

Over the last years, high-throughput technologies have provided the opportunity to explore the genomes of livestock species to identify regions influencing traits of economic interest. Genome wide association studies (GWAS) have been widely used to disentangle the genetic variation in complex phenotypes, such as milk production traits in sheep. The study presented here investigated the possible association of genome-wide SNPs and breeding values for milk production traits in the Valle del Belice sheep. The studied population consisted of a total of 481 ewes belonging to 9 half-sib families with available records for milk yield (MY), protein and fat percentage (P% and F%, respectively). All …

Effect of muscle type and animal category on fatty acid composition of bresaola made from meat of Cinisara cattle: preliminary investigation

The bresaola could represent an alternative commercial opportunity for autochthonous dairy cattle farms. Therefore, a study was carried out to investigate the fatty acid (FA) composition of bresaola made using Semimembranosus (SMm), Semitendinosus (STm), and Biceps brachii (BBm) muscles from grazing young bulls (GB), housed young bulls (HB) or grazing adult cows (AC) of Cinisara breed. Animal category, fat content, feeding system, and type of muscle influenced the FA composition of bresaola. Fatter products, made from AC and HB meat, or with STm and BBm muscles showed lower polyunsaturated/saturated FA ratio. The bresaola from young bulls fed pasture-based diet showed an increased polyunsat…

Stima delle componenti della (co)varianza per il contenuto in cellule (CCS) in pecore di razza Valle del Belice

Additional file 1 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 1: Table S1. Name of the breeds, breed codes, sample size (N), sub-species, continent and geographic origin, and source of genotyping data.

Sistemi agrari

Conservation status and historical relatedness of Italian cattle breeds

Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Ou…

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

The identification of individuals’ breed of origin has several practical applications in livestock and is useful in different biological contexts such as conservation genetics, breeding and authentication of animal products. In this paper, penalized multinomial regression was applied to identify the minimum number of single nucleotide polymorphisms (SNPs) from high-throughput genotyping data for individual assignment to dairy sheep breeds reared in Sicily. The combined use of penalized multinomial regression and stability selection reduced the number of SNPs required to 48. A final validation step on an independent population was carried out obtaining 100% correctly classified individuals. …

Additional file 5 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 5:Tables reporting the P values for the overlapping between goat and cattle CNVRs and among the four CNVR datasets available in cattle. Table S1 reports the results obtained comparing the goat CNVRs with the cattle CNVRs. Table S2 reports the results obtained comparing the different cattle datasets. (DOC 110 KB)

Additional file 2: of Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability

Table S5. Goat haplogroup frequencies based on modern and ancient control-region mtDNA data from this study and downloaded from GenBanka. Table S6. Diagnostic mutational motifs of goat mtDNA haplogroups and sub-haplogroups. Table S7. A comparison of the phylogeographic features of goat, taurine and horse mtDNA haplogroups identified by analyzing domestic breeds from Eurasia. Table S8. Oligonucleotides used to amplify and to sequence (Sanger method) the goat mitochondrial genome. (PDF 652Â kb)

Effect of Mycoplasma agalactiae mastitis on milk production and composition in Valle dell Belice dairy sheep

Contagious agalactia (CA), a disease caused by Mycoplasma agalactiae and other pathogenic mycoplasmas, is a well-known multietiological syndrome affecting dairy breeds of sheep and goats in the Mediterranean basin. The aim of this work was to study the effect on milk production and composition of mastitis caused by M. agalactiae in Valle del Belice dairy sheep. All ewes were manually milked twice daily and the milk from both daily milking was analysed for milk composition and somatic cell counts. Moreover the morning milk samples were collected aseptically from each animal for bacteriological analyses. A mixed linear model was utilised to consider milk production and composition between ani…

Association study between beta-defensin gene polymorphisms and mastitis resistance in Valle del Belice dairy sheep breed

Abstract Mastitis is generally caused by bacteria, and it is the most common disease in livestock species. Defensins are peptides with a broad spectrum of antimicrobial activity and β-defensin genes have been studied in several livestock species due to their important role in the innate immune response. The aim of this study was to establish an association between polymorphisms in the β-defensin 1 and 2 genes and mastitis resistance in the Valle del Belice dairy sheep. Data consisted of 1855 and 2804 observations for case and control group, respectively. Six single nucleotide polymorphisms and seven haplotypes were selected for association studies with mastitis. In particular, polymorphism …

Identification and evaluation of Beta-defensin polymorphisms in Valle del Belice dairy sheep

Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds

The availability of dense single nucleotide polymorphism (SNP) assays allows for the determination of autozygous segments based on runs of consecutive homozygous genotypes (ROH). The aim of the present study was to investigate the occurrence and distribution of ROH in 21 Italian sheep breeds using medium-density SNP genotypes in order to characterize autozygosity and identify genomic regions that frequently appeared in ROH within individuals, namely ROH islands. After filtering, the final number of animals and SNPs retained for analyses were 502 and 46 277 respectively. A total of 12 302 ROH were identified. The mean number of ROH per breed ranged from 10.58 (Comisana) to 44.54 (Valle del B…

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…

Comparison of selection criteria for milk yield traits of Valle del Belice dairy sheep.

Abstract The objectives of this work were to investigate alternative selection criteria for milk yield traits in the Valle del Belice sheep breed, which are either corrected for lactation length or not affected by lactation length, to estimate genetic parameters for these alternative selection criteria and to compare the estimated breeding values. The genetic correlations show that corrected milk yield (CMY), maximum test-day yield (MTY) and milk yield at hundred days (MYH), are moderately or weakly correlated with lactation length (LL) ( r g  = 0.58, 0.16 and 0.39, respectively). Higher genetic correlation was found between total milk yield (TMY) and LL ( r g  = 0.73). Rank correlations be…

Additional file 1 of The genetic heritage of Alpine local cattle breeds using genomic SNP data

Additional file 1: Table S1. Name of the breeds, sample size, breed codes and source of genotyping data.

Study of polymorphisms in the promoter region of ovine β-lactoglobulin gene and phylogenetic analysis among the Valle del Belice breed and other sheep breeds considered as ancestors

The aim of this work was to sequence the promoter region of b-lactoglobulin (BLG) gene in four sheep breeds, in order to identify polymorphisms, infer and analyze haplotypes, and phylogenetic relationship among the Valle del Belice breed and the other three breeds considered as ancestors. Sequencing analysis and alignment of the obtained sequences showed the presence of 36 single nucleotide polymorphisms (SNPs) and one deletion. A total of 22 haplotypes found in ‘‘best’’ reconstruction were inferred considering the 37 polymorphic sites identified. Haplotypes were used for the reconstruction of a phylogenetic tree using the Neighbor-Joining algorithm. The number of polymorphisms identified s…

Genome wide Copy Number Variation (CNV) detection in Cinisara cattle breed

Copy Number Variations (CNVs) are classes of polymorphic genomic regions including deletions, duplications and insertions of DNA fragments from at least 0.5 kb up to several Mb. CNV represents an important source of genetic variability that provides genomics structural information complementary to the single nucleotide polymorphism (SNP) data. Some CNVs have been shown to be important in both normal phenotypic variability and disease susceptibility in livestock. Several approaches to identify CNVs including FISH, aCGH, SNP array or NGS, were proposed and among these SNP genotyping is relatively low cost, high-throughput and high coverage method. The aim of this study was to identify the CNV…

MOESM2 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

Additional file 2: Figure S2. Total number of runs of homozygosity (ROH) longer than 1Â Mb and total length of genome (Mb) covered by ROH segments per individual. Observed (black) vs simulated (red) data.

Short communication: casein haplotype variability in sicilian dairy goat breeds.

In the Mediterranean region, goat milk production is an important economic activity. In the present study, 4 casein genes were genotyped in 5 Sicilian goat breeds to 1) identify casein haplotypes present in the Argentata dell'Etna, Girgentana, Messinese, Derivata di Siria, and Maltese goat breeds; and 2) describe the structure of the Sicilian goat breeds based on casein haplotypes and allele frequencies. In a sample of 540 dairy goats, 67 different haplotypes with frequency >or=0.01 and 27 with frequency >or=0.03 were observed. The most common CSN1S1-CSN2-CSN1S2-CSN3 haplotype for Derivata di Siria and Maltese was FCFB (0.17 and 0.22, respectively), whereas for Argentata dell'Etna, Girgenta…

PRELIMINARY DATA ON HYDROLYTIC ACTIVITY OF LACTIC ACID BACTERIA ON ß-LACTOGLOBULIN IN MILK

β-Lactoglobulin (β-lg) is the major whey milk protein and it represents the main allergen in cow and sheep milk (1). Microbial fermentation produces some proteolytic enzymes and leads to the degradation of milk protein allergens. In this study, the results of a screening on the ability of lactic acid bacteria (LAB) isolated from typical Sicilian cheeses to reduce the β-lg are shown. This screening was carried out through an indirect competitive ELISA. The lactic acid fermentation was found to be suitable for decreasing milk immunoreactivity. Twenty three strains of cheese LAB, belonging to six genera (Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus and Streptococcus), wer…

The genetic heritage of Alpine local cattle breeds using genomic SNP data

Abstract Background Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc an…

Caratterizzazione lattodinamografica del latte di pecore Valle del Belice

Application of the Wood model to lactation curves of Comisana sheep

Abstract Ninety-two ewes of the Comisana breed were used in a study to verify the forecasting capacity of the mathematical model proposed by Wood for fitting sheep data, and to evaluate the effect of the environmental factors affecting the parameters of the lactation curve. The Wood model underestimated the total lactation milk production with an error margin of 12.2 ± 7.8 kg of milk corresponding to 10.9 ± 6.6%. There was a strong influence of order of lambing × lambing season interaction on the lactation parameters. The curves for the winter lambing ewes demonstrated a higher peak production than autumn lambing ewes (1728.4 vs. 1082.6 g, P ≤ 0.05 for the second lambing ewes and 1772.8 vs.…

Stima delle componenti della (co)varianza per il contenuto in cellule somatiche (CCS) in pecore di razza Valle del Belice

An experience in pedigree reconstruction based on likelihood methods using genetic markers

Additional file 15 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Authors’ original file for figure 3

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

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 fo…

Activation of wooden vats with selected lactic acid bacteria for the year-round production of traditional Vastedda-like cheese

Vastedda is a pasta filata cheese made from raw ewes’ milk without the addition of starter cultures. Cheese production is carried out in wooden vats characterized by microbial biofilms hosting lactic acid bacteria (LAB) responsible for the acidification of the curds. Vastedda cheese was traditionally produced during the summer season, but it is currently produced throughout the year. In order to minimize production variability, several LAB were isolated from Vastedda PDO cheeses, characterized for their technological potential (Gaglio et al., 2014a) and selected to obtain the best strain combination for the production (Gaglio et al., 2014b). In this study, the multiple strain culture compos…

Chromosomal assignment of the ovine hairless (hr) gene by fluorescence insitu hybridization

Finocchiaro, F., Castiglioni, B., Budelli, E., van Kaam, J.B.C.H.M., Portolano, B., Caroli, A., Pagnacco, G. 2008.Chromosomal assignment of the ovine hairless (hr) gene by fluorescence in situ hybridization *Hereditas 145: 258 261.Lund, Sweden. eISSN 1601-5223. Received February 25, 2008. Accepted May 26, 2008E-mail: raffaellafinocchiaro@anafi.it

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

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 br…

Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle

AbstractThe availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide. However, these comprehensive studies did not include some local European populations, including autochthonous Italian cattle. In this study, we assembled a large-scale, genome-wide dataset of single nucleotide polymorphisms scored in 3,283 individuals from 205 cattle populations worldwide to assess genome-wide autozygosity and understand better the genetic relationships among these populations. We prioritized European cattle, with a special focus on Italian breeds. Moderate differences in estimates of molecular inbreeding calculated from runs of homozygosity (FROH) were o…

Identification of SNPs in the promoter of β-lactoglobulin gene in three Sicilian goat breeds

The aim of this work was to sequence the full-length promoter region of the caprine &beta;-lactoglobulin (&beta;-lg) gene in three Sicilian goat breeds (Girgentana, Maltese, and Derivata di Siria), in order to identify polymorphisms, to search for transcription factors (TFs) sites, and to check if polymorphisms found lay within TFs binding sites. The promoter region of &beta;-lg gene in Sicilian goat breeds showed high level of polymorphism due to the presence of 31 SNPs. Binding sites for several TFs were found within the goat &beta;-lg promoter and within regions conserved between ovine and caprine species. Two SNPs were detected within TFs binding sites, such as MPBF and NF-I. Further st…

Mastitis susceptibility in Valle del belice ewes related to weather conditions

Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses …

Italian Goat Consortium: a collaborative project to study the Italian caprine biodiversity.

The Italian Goat Consortium (IGC), joined the effort of many Universities and Research Institutes, in a comprehensive study of the Italian goat population genetic makeup using a medium density (54K) SNPs chip. Currently IGC has genotyped more than 1,000 animals from more than 30 goat breeds and populations from all Italian geographical and agroecological areas of goat rearing. The aim of this work is to obtain a clear picture of the Italian caprine biodiversity, to reconstruct the ancestry, to disentangle the genetic background and to assess the relationships among and within the investigated breeds. To date, the IGC dataset includes about 50 million genotypes. The data were quality checked…

Analysis of acetyl-CoA carboxylase gene polymorphisms in Valle del Belice dairy breeds

Acetyl-CoA carboxylase is the flux-determining enzyme in the regulation of fatty acid synthesis within animal tissues. The expression of the mammary gland isoform of this enzyme, during lactation, is regulated by the acetyl-CoA carboxylase-α (ACACA) gene. The ovine ACACA gene, with 51 coding exons, is responsible for phenotypic variability observed in milk fat content and milk fatty acids (FAs) composition. However, before attempting association analyses between this enzyme and phenotypic traits of interest, a study on the genetic variability within this locus is required. The aim of this work was to sequence the encoding region of ACACA gene in Valle del Belice dairy ewes in order to ident…

Casein haplotype variability in Sicilian dairy goat breeds

In the Mediterranean region, goat milk production is an important economic activity. In the present study, 4 casein genes were genotyped in 5 Sicilian goat breeds to 1) identify casein haplotypes present in the Argentata dell'Etna, Girgentana, Messinese, Derivata di Siria, and Maltese goat breeds; and 2) describe the structure of the Sicilian goat breeds based on casein haplotypes and allele frequencies. In a sample of 540 dairy goats, 67 different haplotypes with frequency >or=0.01 and 27 with frequency >or=0.03 were observed. The most common CSN1S1-CSN2-CSN1S2-CSN3 haplotype for Derivata di Siria and Maltese was FCFB (0.17 and 0.22, respectively), whereas for Argentata dell'Etna, Girgenta…

Indici economici per l’allevamento caprino in Sicilia

Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Genetic diversity of Mediterranean cattle breeds related to geography and climate

In recent decades, changes in climate have caused impacts on natural and human systems. Mediterranean countries will be particularly affected by this phenomenon, with growing temperatures and reduced rainfall. Understanding how species and ecosystems respond to climate change has become a crucial focus in biodiversity conservation and management. The genome-wide SNP panels allows providing background information on genome structure in domestic animals, opening new perspectives to livestock genetics. The International Project GALIMED "Genetic Adaptation of Bovine Livestock and production systems in MEDiterranean region", develops an integrated approach that combines the analysis of SNP marke…

Additional file 6 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 6:Primers and PCR conditions used to validate goat CNVRs. The table includes the goat CNVRs number, the corresponding bovine chromosome, gene symbol, amplified gene fragment data (including Ensembl number), sequence of the PCR primers, length of the amnplified fragment and PCR conditions. (DOC 38 KB)

Genome-wide analysis identifies potentially causative genes explaining the phenotypic variability in Pinzirita sheep

Genome-wide analysis identifies potentially causative genes explaining the phenotypic variability in Pinzirita sheep

Lactation curves in Valle del Belice sheep using random regression models

Cellule somatiche in latte ovino: analisi e applicazione delle curve ROC

Negli ovini da latte le mastiti costituiscono una delle principali cause di perdite economiche per la ridotta produzione e soprattutto per la scarsa qualità tecnologica del latte. Diversi studi hanno dimostrato che il contenuto in cellule somatiche (SCC) del latte può essere impiegato sia come metodo diagnostico sia come criterio di selezione nei programmi di miglioramento genetico per la resistenza alle mastiti. Obiettivo di questo lavoro è stato applicare la metodologia delle Receiver Operating Characteristics curves (ROC) per valutare la capacità diagnostica del SCC nel discriminare le mammelle infette da quelle sane e per individuare un valore soglia discriminante in ovini da latte. In …

STUDY OF MASTITIS IN DAIRY SHEEP USING SURVIVAL ANALYSIS

Mastitis is the most prevalent disease present in livestock species leading to economic loss. In dairy sheep, it caused mainly from bacterial infections. The aim of this work was to investigate the risk of having mastitis in Valle del Belice dairy ewes during the first lactation, due to environmental or contagious pathogens, using a survival analysis approach. All test‐day records from primiparous ewes were collected from five flocks. All test‐day were grouped in two data sets, one with mastitis due to environmental pathogens (ENV) and the other with mastitis due to contagious pathogens (CON). In this analysis the follow up period of a ewe was the lactation, consequently all the record bega…

Effect of beta-lactoglobulin polymorphism on milk-related traits of dairy ewes analysed by a repeated measures design.

Among specific genes that may affect economically important traits in sheep, the β-lactoglobulin (LGB) locus has been extensively studied. Polymorphism has been detected in several breeds, but studies of the effect of LGB alleles on milk production traits have given conflicting results. Some found that LGB polymorphism significantly affects milk yield (Bolla et al. 1989; Herget et al. 1995; Fraghì et al. 1996), fat and protein content (Garzon &amp; Martínez 1992; Giaccone et al. 1997; Kukovics et al. 1998), only fat content (Pirisi et al. 1998) and cheese yield and composition (Di Stasio et al. 1997; Rampilli et al. 1997). However, other studies failed to detect any effect of the gene on mi…

GoMilkSicily: an opportunity for transfer of knowledge

Polymorphisms at β-defensin genes and mastitis in Valle del Belice dairy sheep: a case control study

Mastitis is the most common and costly pathology affecting dairy animals. The identification of genetic markers that allow the inclusion of mastitis resistance in selection programs would help to reduce the costs due to the disease and the use of antibiotics. In recent years, β-defensin genes have been studied in several domestic species due to their important role in the innate immune response. The aim of this study was to determine whether β-defensin genes variability, β-defensin 1 (SBD1) and β-defensin 2 (SBD2), could distinguish between infected cases and healthy controls in Valle del Belice dairy sheep. Somatic cell count (SCC) is a powerful tool to identify animals with intramammary i…

Time-to-event analysis of mastitis at first-lactation in Valle del Belice ewes

A time-to-event study for mastitis at first-lactation in Valle del Belice ewes was conducted, using survival analysis with an animal model. The goals were to evaluate the effect of lambing season and level of milk production on the time from lambing to the day when a ewe experienced a test-day with a recorded SCC greater than or equal to 750,000 cells/ml, and to estimate, for this trait, its heritability and the percentage of variation explained by the flock-year of lambing effect. A dataset with 2468 first-lactation records, collected from 1998 to 2003 in Valle del Belice ewes allocated in 17 flocks, was used. The Cox model used included lambing season and total milk yield adjusted for lac…

PrP allele frequencies in non-infected Valle del Belice and infected cross-bred flocks

Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds

Background The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array. Results Average r2 between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Ave…

MOESM3 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

Additional file 3: Figures S3, S4, S5, S6. Plot of SNP occurrences (%) in ROH against the genomic regions of QTL for OAR chromosomes with the highest inbreeding coefficient (OAR 2, 4, 11, 23).

Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds

Runs of homozygosity (ROH) are widely used as predictors of whole-genome inbreeding levels in cattle. They identify regions that have an unfavorable effect on a phenotype when homozygous, but also identify the genes associated with traits of economic interest present in these regions. Here, the distribution of ROH islands and enriched genes within these regions in four dairy cattle breeds were investigated. Cinisara (71), Modicana (72), Reggiana (168) and Italian Holstein (96) individuals were genotyped using the 50K v2 Illumina BeadChip. The genomic regions most commonly associated with ROHs were identified by selecting the top 1% of the single nucleotide polymorphisms (SNPs) most commonly…

Analysis of runs of homozygosity of cattle living in different climate zones

Abstract Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds’ country of…

Assessment of genetic variation for pathogen-specific mastitis resistance in Valle del Belice dairy sheep

Background: Mastitis resistance is a complex and multifactorial trait, and its expression depends on both genetic and environmental factors, including infection pressure. The objective of this research was to determine the genetic basis of mastitis resistance to specific pathogens using a repeatability threshold probit animal model. Results: The most prevalent isolated pathogens were coagulase-negative staphylococci (CNS); 39 % of records and 77 % of the animals infected at least one time in the whole period of study. There was significant genetic variation only for Streptococci (STR). In addition, there was a positive genetic correlation between STR and all pathogens together (ALL) (0.36 ±…

An initial comparative map of copy number variations in the goat (Capra hircus) genome

Abstract Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi,…

Coat colours in the Massese sheep breed are associated with mutations in the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes

Massese is an Italian dairy sheep breed characterized by animals with black skin and horns and black or apparent grey hairs. Owing to the presence of these two coat colour types, this breed can be considered an interesting model to evaluate the effects of coat colour gene polymorphisms on this phenotypic trait. Two main loci have been already shown to affect coat colour in sheep: Agouti and Extension coding for the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes, respectively. The Agouti locus is affected by a large duplication including the ASIP gene that may determine the Agouti white and tan allele (A(Wt)). Other disrupting or partially inactivating mutations ha…

Copy Number Variation and Missense Mutations of the Agouti Signaling Protein (&lt;i&gt;ASIP)&lt;/i&gt; Gene in Goat Breeds with Different Coat Colors

In goats, classical genetic studies reported a large number of alleles at the &lt;i&gt;Agouti&lt;/i&gt; locus with effects on coat color and pattern distribution. From these early studies, the dominant &lt;i&gt;A&lt;/i&gt;&lt;sup&gt;Wt&lt;/sup&gt; (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat &lt;i&gt;ASIP&lt;/i&gt; gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-ri…

Identification of SNPs and copy number variation in goat MC1R and ASIP genes: an association study with coat colour in a few Mediterranean goat breeds

Identification of breed informative single nucleotide polymorphisms for assigning individual in Sicilian dairy sheep

Assignment tests using genetic information to establish population membership of individuals, provide the most direct methods to determine the population of origin of unknown individuals. The identification of the breed or population of origin of individuals potentially offers unbiased tools in livestock and is useful in a variety of biological contexts. The aim of this study was to identify the minimum number of informative SNPs from highthroughput genotyping data in Sicilian dairy sheep breeds, and to investigate their usefulness for breed assignment purposes. Individuals of Valle del Belice (48), Comisana (48) and Pinzirita (53) sheep breeds were genotyped using Illumina OvineSNP50K Geno…

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 …

Analysis of milk production of Valle del Belice ewes reared in their area of origin and analysis of expansion of the breed

Linkage disequilibrium and genetic diversity estimation in three Sicilian autochthonous dairy sheep breeds

Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. In the present study, we used the OvineSNP50K BeadChip to characterize LD, identify haplotype blocks and to analyze genetic diversity in the Valle del Belice (VDB), Comisana (COM) and Pinzirita (PIN) dairy sheep breeds. LD between adjacent SNPs and for all pairwise combinations of SNPs on each chromosome was measured using r2. Haplotype blocks were estimated using D’ based method. Genetic diversity and Principal Component Analysis (PCA) were calculated using PLINK. Small differences in average LD value for adjace…

In vivo application and dynamics of lactic acid bacteria for the four-season production of Vastedda-like cheese.

article Twelve lactic acid bacteria (LAB), previously selected in vitro (Gaglio et al., 2014), were evaluated in situ for their potential to act as starter cultures for the continuous four-season production of Vastedda-like cheese, made with raw ewes' milk. The strains belonged to Lactobacillus delbrueckii, Lactococcus lactis subsp. cremoris, Leuconostoc mesenteroides subsp. mesenteroides and Streptococcus thermophilus .L AB werefirst inoculated in multiple-strain combinations on the basis of their optimal growth temperatures in three process conditions which differed for milk treatment and medium for strain development: process 1, growth of strains in the optimal synthetic media and pasteu…

Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage.

The mitochondrial hypervariable region 1 (HVR1) sequence of 67 goats belonging to the Girgentana, Maltese and Derivata di Siria breeds was partially sequenced in order to present the first phylogenetic characterization of Sicilian goat breeds. These sequences were compared with published sequences of Indian and Pakistani domestic goats and wild goats. Mitochondrial lineage A was observed in most of the Sicilian goats. However, three Girgentana haplotypes were highly divergent from the Capra hircus clade, indicating that a new mtDNA lineage in domestic goats was found.

Genetic structure and assignment test in five sheep breeds reared in Sicily using microsatellites

A total of 331 individuals from five sheep breeds reared in Sicily (Barbaresca (BAR, n=57), Comisana (COM, n=65), Pinzirita (PIN, n=75), Sarda (SAR, n=64), and Valle del Belice (VdB, n=70)) were analysed to investigate genetic structure and perform an assignment test. A panel of 20 microsatellite markers was used, and a total of 259 alleles were observed. The polymorphic information content (PIC) all over loci was equal to 0.757, showing that the microsatellites panel used was highly informative. Estimates of observed heterozygosity ranged from 0.655 in the BAR breed to 0.751 in the COM breed. The low value of genetic differentiation among breeds (FST=0.048) may indicate that these breeds a…

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

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…

MOESM1 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

Additional file 1: Figure S1. Mean sum of runs of homozygosity (ROH) per animal estimated within four different generation categories. ROH were mapped according to their genetic positions (i.e. linkage map positions). ROH length (l cM) within each category was determined using 100/2 g, replacing g with the number of generations of interest.

Comparative selection signature analyses identify genomic footprints in Reggiana cattle, the traditional breed of the Parmigiano-Reggiano cheese production system

Reggiana is an autochthonous cattle breed reared mainly in the province of Reggio Emilia, located in the North of Italy. Reggiana cattle (originally a triple-purpose population largely diffused in the North of Italy) are characterised by a typical solid red coat colour. About 2500 cows of this breed are currently registered to its herd book. Reggiana is now considered a dual-purpose breed even if it is almost completely dedicated to the production of a mono-breed branded Protected Designation of Origin Parmigiano-Reggiano cheese, which is the main driver of the sustainable conservation of this local genetic resource. In this study, we provided the first overview of genomic footprints that c…

Development of "Quadrello di Ovino", a Novel Fresh Ewe's Cheese.

This work was performed to produce a new soft ewe’s milk cheese, namely “Quadrello di ovino” (QdO) cheese, to enlarge ewe’s dairy product portfolio of South Italy, barely limited to Pecorino cheese typology. Cheese making was performed applying the technology for “Crescenza” cheese typology with some modifications. In particular, pasteurized ewes’ milk was inoculated with two commercial starter formulations (SF1 and SF2) of Streptococcus thermophilus to obtain two different productions (QdO-P1 and QdO-P2, respectively). Plate counts demonstrated the ability of both starter formulations to drive the fermentation process, since S. thermophilus counts reached 109 CFU/g in both productions. Gen…

Molecular characterisation of k-casein gene in Girgentana dairy goat breed and identification of two new alleles

The k-casein fraction plays an important role in the formation, stabilisation and aggregation on casein micelles and thus affects technological and nutritional properties of milk. In this study, exon 4 of k-casein (CSN3) gene was sequenced and analysed in Girgentana goat breed. Analyses of the obtained sequences showed the presence of A, B, D, and G known alleles and two new genetic variants, named D’ and N. The new D’ allele differs from D in one transition, G284→A284, which did not cause amino acid change. The new N allele differs from A in five single nucleotide polymorphisms (SNPs): T245/C245, G284/A284, G309/A309, G471/A471 and T591/C591, while it differs from C in one transition, i.e.…

Effect of hairless gene polymorphism on the breeding values of milk production traits in Valle del Belice dairy sheep

The aim of this work was to assess the association between the hairless genotypes and estimated breeding values (EBVs) for milk yield (MY), fat (FAT) and protein (PRT) content in Valle del Belice dairy sheep breed. A data set from 465 randomly chosen unrelated individuals was analyzed. EBV for MY, FAT and PRT contents were estimated by REML analysis of a single trait repeatability animal model. The genotype effect on EBV was assessed by ANOVA and by the Tukey–Kramer multiple comparison test. The PCR-SSCP test showed the presence of CC and CT genotypes in Valle del Belice individuals. Some differences in milk production traits between the genotypes were found. For MY, individuals with CT gen…

Genetic polymorphism at the CSN1S1 gene in Girgentana dairy goat breed

The aim of this work was to evaluate the variability of the αs1-casein locus in the endangered Girgentana dairy goat breed in order to define genetic improvement and a conservation program for this breed. The study was performed on 200 dairy goats by means of different PCR protocols. The most frequent alleles were A (0.590) and F (0.290) followed by B (0.065) and N (0.047). CSN1S1 E allele was identified with a very low frequency (0.008). The most common genotype was AF (0.365) followed by AA (0.340). The high frequency of the strong genotypes is associated with the production of milk with high fat and protein content and with optimal technological properties. In Girgentana goat breed, the …

MOESM8 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 8: Figure S5. Cross-validation errors of admixture analysis at different K values.

The Sicilian cattle breeds in a global context: genome-wide relationship with other worldwide cattle

Genomic technologies, such as high-throughput genotyping based on Single Nucleotide Polymorphism (SNP) arrays, provide background information concerning genome structure in domestic animals. The aims of this study were to cluster animals, to explore the relationships among and within breeds, and to place the Sicilian breeds, Cinisara and Modicana, in a global context. The Illumina Bovine SNP50K v2 BeadChip genotyping data from 144 animals of Sicilian breeds and from other 1,543 animals belonging to 134 domesticated bovid breeds (DRYAD) were used. These breeds arose from 3 domesticated (sub)species: Bos javanicus, B. taurus indicus, and B. t. taurus. Principal Component Analysis (PCA) genera…

Analyses of udder health in Valle del Belice dairy sheep using SCC

Intramammary infections (IMI) are a complex of inflammatory diseases of the mammary gland. Mastitis is one of the most frequent IMI affecting small dairy ruminants. Direct selection against clinical mastitis is difficult because mastitis in not widely recorded; therefore, somatic cell count (SCC) is promoted as selection criterion for mastitis resistance. A dataset containing 2,457 first- lactation Valle del Belice ewes from 14 flocks recorded from 1998 to 2003 was analysed. In total 116 sires with at least four daughters with a record were included in the pedigree file. Test-day IMI events were coded as a binary trait using a SCC cut-off value of 750,000 cells/ml. Analyses of risk factors …

A first comparative map of copy number variations in the sheep genome.

article i nfo We carried out a cross species cattle-sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in cattle a…

MOESM4 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

Additional file 4: Figure S7. Plot of SNP occurrences in ROH against recombination rate. Recombination rate is the solid red line and the occurrence of a SNP in a ROH is represented by blue dots. (A) OAR2, (B) OAR4, (C) OAR11, and (D) OAR23. Recombination rate (cM/Mb) was estimated every 500Â kb.

La messinese una risorsa autoctona tutta siciliana

Genetic and Environmental components of susceptibility to heat stress in mediterranean dairy sheep

Comparison of casein haplotypes between two geographically distant European dairy goat breeds.

The aim of this paper was to characterize the diversity among haplotypes based on 22 single nucleotide polymorphisms (SNPs) and one deletion within four casein genes in two geographically distant goat populations, the Sicilian Girgentana breed and the Norwegian goat breed. Forty Girgentana goats were genotyped for the aforementioned polymorphisms and the resulting data set was compared with 436 goats from the Norwegian population previously genotyped for these markers. Several casein gene polymorphisms were not in Hardy-Weinberg equilibrium either in Girgentana, or in the Norwegian breed. The SNP haplotype frequencies for the four casein genes were calculated and despite the large geographi…

Genetic parameters for somatic cell score according to udder infection status in Valle del Belice dairy sheep

Demographic characterization and genetic variability of the Oriental Pure Horse, reared in Sicily, by genealogical data analysis

GeneticParameters for Milk Somatic Cell Score and Relationships with Production Traits in Primparous Dairy Sheep

A total of 13,066 first-lactation test-day records of 2,277 Valle del Belice ewes from 17 flocks were used to estimate genetic parameters for somatic cell scores (SCS) and milk production traits, using a repeatability test-day animal model. Heritability estimates were low and ranged from 0.09 to 0.14 for milk, fat, and protein yields, and contents. For SCS, the heritability of 0.14 was relatively high. The repeatabilities were moderate and ranged from 0.29 to 0.47 for milk production traits. The repeatability for SCS was 0.36. Flock-test-day explained a large proportion of the variation for milk production traits, but it did not have a big effect on SCS. The genetic correlations of fat and …

Additional file 8 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 8:Gene Ontology (GO) annotation of genes included in goat CNVRs. Ensembl cattle transcripts located in goat CNVRs have been annotated using GO for Biological process, Cellular component, and Molecular function. (XLS 108 KB)

MOESM12 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 12: Table S5. Results of the f4 test.

MOESM5 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

Additional file 5: Table S1. List of 239 SNPs considered as candidate markers under directional selection in the Valle del Belice sheep breed.

Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 8 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 8: Figure S6. Increment in the log likelihood for the reduced (European taurine and the Guelmoise) dataset for all tested migration events, calculated by using the optM function in the R package OptM.

Additional file 5 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 5: Figure S3. Cross-validation plot of the admixture analysis for all values of K (number of clusters) ranging from 2 to 23.

MOESM11 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 11: Table S4. Results of the f3 test.

Additional file 2 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 2: Figure S1. All modelled scenarios for colonization tested in the ABC framework. Description: In all the tested scenarios, we assumed that taurine and indicine cattle separated first. Subsequent reduction in effective population size was modelled to take the two independent domestication events that occurred in the Fertile Crescent and the Indus Valley into account. From these known evolutionary events, two sets of scenarios were built. The first three scenarios mirror to two different waves of migration, an early Neolithic migration involving non-Podolian taurine cattle and a secondary migration involving Podolian cattle after their genetic admixture with indicine cattle …

Additional file 12 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 12:List of goat CNVRs with human orthologous genes. EntrezGene ID and gene name are reported for human orthologous genes. The file includes genes already mapped in goat and genes for which mutations in human cause or are associated with human genetic diseases (data have been retrieved from OMIM database, May 2010). (XLS 60 KB)

Additional file 16 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Authors’ original file for figure 4

Additional file 3 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 3:Extension of CNVRs in the different chromosomes. Proportion of the CNVRs identified in goat compared to the dimension of the bovine chromosomes. (XLS 14 KB)

Additional file 3 of The genetic heritage of Alpine local cattle breeds using genomic SNP data

Additional file 3: Figure S2. Admixture analysis plot in a circular fashion with all values of K (number of clusters) ranging from 2 to 28.

Additional file 5 of The genetic heritage of Alpine local cattle breeds using genomic SNP data

Additional file 5: Figure S3. Increment in the log likelihood for all tested migration events calculated by using the optM function in the R package OptM.

Additional file 9 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 9: Figure S7. Principal component analysis (PCA) for the two datasets used (17 K and 8 K).

Additional file 7 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 7: Figure S5. Increment in the log likelihood for the complete dataset for all tested migration events, calculated by using the optM function in the R package OptM.

Additional file 14 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Authors’ original file for figure 2

Additional file 2 of The genetic heritage of Alpine local cattle breeds using genomic SNP data

Additional file 2: Figure S1. Cross-validation plot of admixture analysis for all values of K (number of clusters) ranging from 2 to 28.

Additional file 7 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 7:Semiquantitative fluorescent multiplex-PCR (SQF-PCR) results obtained for different goats. The averaged SQF-PCR ratio normalized against the reference Camosciata delle Alpi goat is reported for the goats of the aCGH panel and for additional goats (additional panel) for the validated CNVs. (XLS 20 KB)

Additional file 9 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 9:PANTHER annotation of genes included in goat CNVRs. Ensembl cattle transcripts located in goat CNVRs have been annotated using PANTHER. (XLS 102 KB)

Additional file 1: of Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability

Table S1. Sources for the 758 goat control-region sequences. Table S2. Control-region haplotypes and haplogroup classification of the 758 mtDNA sequences from Capra aegagrus (n = 19) and Capra hircus (n = 739). Table S3. Partial coding-region haplotypes and haplogroup classification of two bezoar mtDNAs. Table S4. Source and haplogroup affiliation of the goat complete mtDNA sequences. Figure S1. Nucleotide diversity and total number of substitutions along the entire mtDNA. Figure S2. A putative most parsimonious tree of 84 complete mtDNA sequences from goats. (XLSX 1268 kb)

MOESM6 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

Additional file 6: Table S2. List of 107 potential candidate genes under directional selection in the Valle del Belice sheep breed.

Additional file 4 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 4:List of cattle CNVRs reported in four other experiments[49–52]and overlapping with goat CNVRs. CNVRs identified in cattle have been merged from the four reported experiments [49–52]. Progressive CNVR number has been assigned using the complete list. CNVRs are indicated with nucleotide positions (begin and end) on the Btau_4.0 version. Information reported for the four different experiments includes the progressive number and in parenthesis the chromosome number and the nucleotide positions (start and end). The goat CNVRs are reported. (XLS 128 KB)

Additional file 1 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 1:List of CNVs identified in the analysed goats. The Excel file reports the chromosome, the nucleotides position of the CNV start and end (referred to the Btau_4.0 genome assembly), the size of the CNV in bp, the number of valid probes in the CNV (additional probes are included in CNV considering the position between two contiguous regions without 0.175 log2 value; see Methods for the definition of CNV), log2 mean of the probes in the CNV (see Methods), the type of CNV (gain/loss), the goat sample (C = Camosciata delle Alpi; G = Girgentana; MG = Murciano-Granadina; S = Saanaen; numbers after the breed symbols indicate the different animals used in the aCGH experiment), and t…

Additional file 17 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Authors’ original file for figure 5

Variation of proteomic profile during lactation in Girgentana goat milk: a preliminary study

The knowledge of milk proteome has been greatly enhanced by technological advances in the proteomics field as the use of the two-dimensional differential in-gel electrophoresis, a gel-based approach which allowed the analysis of proteins from complex mixtures and the comparing of several protein samples in the same experiment. The aim of this study was to characterise the whole milk proteomic profile in Girgentana dairy goat breed by two-dimensional differential in-gel elecrophoresis. The obtained representative 2D whole milk proteomic map showed a general picture of the protein distributions over the pH 3–10 NL including about 100 spots, most of them organised like a spot train. Among diff…

Additional file 13 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Authors’ original file for figure 1

MOESM5 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 5: Figure S2. Relationship between the number of ROH and the length of the genome (Mb) covered by ROH per individual.

MOESM9 of Conservation status and historical relatedness of Italian cattle breeds

Additional file 9: Table S3. Pairwise FST values between cattle populations.

Additional file 6 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 6: Figure S4. Admixture analysis plot in a circular fashion with all values of K (number of clusters) ranging from 2 to 23.

Additional file 2 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 2:List of CNVRs obtained by merging overlapping CNVs across animals. The Excel file reports the progressive CNVR number, the chromosome, the nucleotides position of the CNVR start and end (referred to the Btau_4.0 genome assembly), the size of the CNVR in bp, the number of valid probes in the CNVR (additional probes are included in CNVR considering the position between two contiguous regions without 0.175 log2 value; see Methods for the definition of CNVR), the type of CNVR (gain/loss), the frequency of CNVR in the analysed goat panel, the goat breed (C = Camosciata delle Alpi; G = Girgentana; MG = Murciano-Granadina; S = Saanaen), and the goat subject (numbers after the bre…

Additional file 4 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 4: Figure S2. Genetic diversity indices: observed and expected heterozygosity (Ho and He), effective population size (Ne) and minor allele frequencies (MAF) calculated for each breed. Asian indicine (blue), African taurine (yellow), European Podolian (orange), European non-Podolian (red).