0000000000002002
AUTHOR
Salvatore Mastrangelo
showing 171 related works from this author
Preselection statistics and Random Forest classification identify population informative single nucleotide polymorphisms in cosmopolitan and autochth…
2018
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 …
Genome-wide scan of fat-tail sheep identifies signals of selection for fat deposition and adaptation
2018
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 …
Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
2021
Abstract Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italia…
Genome-wide association study reveals the locus responsible for microtia in Valle del Belice sheep breed.
2018
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…
Genome-wide detection of signatures of selection in three Valdostana cattle populations
2020
International audience; The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (F-ST) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least tw…
High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources
2023
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…
Genome-wide analysis in endangered populations: a case study in Barbaresca sheep
2017
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…
Genome-wide assessment of diversity and differentiation between original and modern Brown cattle populations
2020
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…
Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds
2021
The aim of this study was to conduct a genome-wide comparative analysis of 8 local Italian chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo [PML], Polverara Bianca, Polverara Nera, Padovana, Pepoi [PPP], Robusta Lionata, and Robusta Maculata), all under a conservation plan, to understand their genetic diversity and population structure. A total of 152 animals were analyzed using the Affymetrix Axiom 600 K Chicken Genotyping Array. The levels of genetic diversity were highest and lowest in PML and PPP, respectively. The results of genomic inbreeding based on runs of homozygosity (ROH; FROH) showed marked differences among breeds and ranged from 0.161 (PML) to 0.478 (PPP). Furtherm…
Genome-wide association studies for milk production traits in Valle del Belice sheep using repeated measures
2019
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 …
Genome-wide diversity of Pagliarola sheep residual population and its conservation implication
2021
Local breeds represent an underestimated resource in terms not only of their important cultural and economical role in marginal areas, but also because they often own a potential genetic pool well adapted to extreme conditions. This fact is of increasing interest, especially when considering climate global challenges where peculiar and uncommon traits could be advantageous. In this study, we genotyped 24 individuals belonging to the small residual Pagliarola sheep population using the OvineSNP50K array, in order to compare its genomic architecture with other 21 Italian local breeds. Moreover, we performed the fixation index (FST) outlier analysis to identify genes most differentiated betwee…
Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds.
2022
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 …
Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chicke…
2023
Abstract Background Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homoz…
On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
2021
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…
Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping
2021
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 …
The genome-wide structure of two economically important indigenous Sicilian cattle breeds1
2014
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.
2019
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…
Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds
2016
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…
Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds
2018
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. …
The Sicilian rock partridge: latest data on genetic integrity from four different relict areas
2021
Sicily (Italy) hosts a “relict”, endemic population of the birds Alectoris graeca whitakeri commonly known as Sicilian Rock Partridge. In the last decades, due to the risk of restocking with other European and Asiatic species for hunting purpose, a study was carried out to investigate the potential risk of hybridisation. The mtDNA control-region and nuclear microsatellites were genotyped. Due to the importance of the species, samples were mainly characterized by feather and stool samples, and rarely by carcasses found in the environment, from year 2011 to 2012. A panel of 7 microsatellite loci was validated. Three multiplexes that allowed the simultaneous amplification of 3 microsatellites,…
The genetic heritage of Alpine local cattle breeds using genomic SNP data
2020
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…
A genome‐wide comparison between selected and unselected Valle del Belice sheep reveals differences in population structure and footprints of recent …
2023
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…
Genome-Wide Association Study Identifies New Candidate Markers for Somatic Cells Score in a Local Dairy Sheep
2021
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 c…
2020
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…
Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle
2021
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 …
Genetic structure of Tunisian sheep breeds as inferred from genome-wide SNP markers
2020
Abstract Assessing the status of genetic variability of native sheep breeds could provide important clues for research and policy makers to devise better strategies for the conservation and management of genetic resources. In this study, a genetic investigation of Tunisian sheep breeds using a genome-wide scan of approximately 50,000 SNPs was performed. To reconstruct genetic structure and relationships among four sheep breeds, 40 samples belonging to fat-tailed Barbarine, Queue Fine de l’Ouest, Noire de Thibar and D’Man breeds were genotyped using Illumina Ovine SNP50 BeadChip. Tunisian breeds averaged 96 % polymorphic loci with an expected heterozygosity (He = 0.36). Genetic analysis of r…
Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds
2018
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
2023
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…
A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds
2023
Abstract Background To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. Results The results indicate…
The genetics of phenotypic plasticity in livestock in the era of climate change: a review
2020
Climate change has the potential to adversely affect the health of livestock, with consequences to animal welfare, greenhouse gas emissions, productivity, human health and livelihoods. Phenotypic plasticity is the ability of a genotype to produce different phenotypes, depending on environmental, biotic or abiotic conditions; it is a factor influencing and modifying the genes of animal and plant organisms, to adaptation to climate change. Among the various climate variables, heat stress has been reported to be the most detrimental factor to the economy of the livestock industry. There are a number of candidate genes that are associated with adaptation of ruminants, monogastric and poultry to…
Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area.
2021
Abstract Under a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale genetic structure and for detecting genomic regions under selection in 63 Tunisian sheep samples. The average genomic inbreeding coefficients based on ROH were estimated at 0.017, 0.021, and 0.024 for Barbarine (BAR, n = 26), Noire de Thibar (NDT, n = 23), and Queue fine de l'Ouest (QFO, n = 14) breeds, respectively. The genomic relationships among individuals based on identity by state (I…
Genome-wide association study for milk production traits in an economically important local dairy sheep breed
2021
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…
Comparative selection signature analyses identify genomic footprints in Reggiana cattle, the traditional breed of the Parmigiano-Reggiano cheese prod…
2020
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…
Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity in local North African cattle
2020
International audience; Natural-driven selection is supposed to have left detectable signatures on the genome of North African cattle which are often characterized by the fixation of genetic variants associated with traits under selection pressure and/or an outstanding genetic differentiation with other populations at particular loci. Here, we investigate the population genetic structure and we provide a first outline of potential selection signatures in North African cattle using single nucleotide polymorphism genotyping data. After comparing our data to African, European and indicine cattle populations, we identified 36 genomic regions using three extended haplotype homozygosity statistic…
Genome‐wide survey on three local horse populations with a focus on runs of homozygosity pattern
2022
Purosangue Orientale Siciliano, Sanfratellano and Siciliano represent the Sicilian equine genetic resource. This study aimed to investigate the genetic diversity, population structure and the pattern of autozygosity of Sicilian horse populations using genome-wide single-nucleotide polymorphism (SNP) data generated with the Illumina Equine SNP70 array. The genotyping data of 17 European and Middle East populations were also included in the study. The patterns of genetic differentiation, model-based clustering and Neighbour-Net showed the expected positioning of Sicilian populations within the wide analysed framework and the close connections between the Purosangue Orientale Siciliano and the…
Genetic diversity and population structure of Sicilian sheep breeds using microsatellite markers
2012
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…
How Geography and Climate Shaped the Genomic Diversity of Italian Local Cattle and Sheep Breeds
2022
International audience; Understanding the relationships among geography, climate, and genetics is increasingly important for animal farming and breeding. In this study, we examine these inter-relationships in the context of local cattle and sheep breeds distributed along the Italian territory. To this aim, we used redundancy analysis on genomic data from previous projects combined with geographical coordinates and corresponding climatic data. The effect of geographic factors (latitude and longitude) was more important in sheep (26.4%) than that in cattle (13.8%). Once geography had been partialled out of analysis, 10.1% of cattle genomic diversity and 13.3% of that of sheep could be ascribe…
Development and validation of RP-HPLC method for the quantitative estimation of αs1-genetic variants in goat milk
2013
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.…
Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia
2018
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…
Genetic variability at αs2-casein gene in Girgentana dairy goat breed
2014
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…
12S rRNA mitochondrial gene as marker to trace Sicilian mono-species dairy products
2016
Abstract For a rapid, specific and sensitive identification of cows', ewes' and goats' milk in mono-species Sicilian dairy products, species-specific duplex-PCR protocol was applied. DNA samples from blood and experimental cheeses of Sicilian autochthonous breeds were extracted to amplify the 12S rRNA (and part of 16S rRNA in case of Ovis aries ) mitochondrial species-specific gene fragment. The use of species-specific primers for Bos taurus , Capra hircus and Ovis aries species, after electrophoresis on agarose gel, yielded fragments of 256 bp, 326 bp and 172 bp, respectively. Amplification by duplex - PCR of DNA pools from two species showed detection thresholds of 0.1% of “contaminant” D…
Genetic characterisation of CSN2 gene in Girgentana goat breed
2014
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…
A genomic map of climate adaptation in Mediterranean cattle breeds
2019
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…
Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat
2022
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…
Genomic characterization of Algerian Guelmoise cattle and their genetic relationship with other North African populations inferred from SNP genotypin…
2018
International audience; Understanding between and within-breeds genetic variability is essential in the choice of conservation management decisions for threatened populations. In this study we assessed the genetic diversity of the Algerian Guelmoise cattle (GUE) by analyzing data on 24 GUE individuals genotyped for the Illumina BovineSNP50 BeadChipv2. We also provided a detailed description of the population structure of GUE using comparisons with 23 worldwide cattle populations, selected as being representative of African, South European and indicine populations, in addition to four North African populations. We show that GUE is an admixed population which has strong genetic similarity to …
Determination of milk production losses and variations of fat and protein percentages according to different levels of somatic cell count in Valle de…
2018
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: …
Population genetic structure and milk production traits in Girgentana goat breed
2017
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…
Genome-wide variation, candidate regions and genes associated with fat deposition and tail morphology in Ethiopian indigenous sheep
2019
Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, which have impacted on the variation of its indigenous livestock. Here, we investigate autosomal genome-wide profiles of 11 Ethiopian indigenous sheep populations using the Illumina Ovine 50 K SNP BeadChip assay. Sheep from the Caribbean, Europe, Middle East, China, and western, northern and southern Africa were included to address globally, the genetic variation and history of Ethiopian populations. Population relationship and structure analysis se…
Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
2017
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…
Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations.
2021
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 >
Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep.
2019
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…
A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds.
2019
Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical F-ST-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested via the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, …
Genomic structural diversity in local goats: Analysis of copy-number variations
2020
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
2020
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…
Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds
2022
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…
Genome-wide detection of copy-number variations in local cattle breeds
2019
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…
Parentage verification of Valle del Belice dairy sheep using multiplex microsatellite panel
2013
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,…
Genomic characterization of the Braque Français type Pyrénées dog and relationship with other breeds
2018
The evaluation of genetic variability is a useful research tool for the correct management of selection and conservation strategies in dog breeds. In addition to pedigree genealogies, genomic data allow a deeper knowledge of the variability and genetic structure of populations. To date, many dog breeds, such as small regional breeds, still remain uncharacterized. Braque Français type Pyrénées (BRA) is a dog breed originating from a very old type of gun-dog used for pointing the location of game birds to hunters. Despite the ancient background, the knowledge about levels of genetic diversity, degree of inbreeding and population structure is scarce. This may raise concerns on the possibility …
A combined genome-wide approach identifies a new potential candidate marker associated with the coat color sidedness in cattle
2019
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…
Quantitative determination of casein genetic variants in goat milk: Application in Girgentana dairy goat breed
2016
The study was conducted to develop a high-performance liquid chromatographic (HPLC) method to quantify casein genetic variants (αs2-, β-, and κ-casein) in milk of homozygous individuals of Girgentana goat breed. For calibration experiments, pure genetic variants were extracted from individual milk samples of animals with known genotypes. The described HPLC approach was precise, accurate and highly suitable for quantification of goat casein genetic variants of homozygous individuals. The amount of each casein per allele was: αs2-casein A = 2.9 ± 0.8 g/L and F = 1.8 ± 0.4 g/L; β-casein C = 3.0 ± 0.8 g/L and C1 = 2.0 ± 0.7 g/L and κ-casein A = 1.6 ± 0.3 g/L and B = 1.1 ± 0.2 g/L. A good correl…
Weighted Single-Step Genome-Wide Association Study Uncovers Known and Novel Candidate Genomic Regions for Milk Production Traits and Somatic Cell Sco…
2022
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 …
Variation of proteomic profile during lactation in Girgentana goat milk: a preliminary study
2019
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
2017
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 …
Genome-wide diversity and runs of homozygosity in the “Braque Français, type Pyrénées” dog breed
2018
Objective Braque Français, type Pyrénées is a French hunting-dog breed whose origin is traced back to old pointing gun-dogs used to assist hunters in finding and retrieving game. This breed is popular in France, but seldom seen elsewhere. Despite the ancient background, the literature on its genetic characterization is surprisingly scarce. A recent study looked into the demography and inbreeding using pedigree records, but there is yet no report on the use of molecular markers in this breed. The aim of this work was to genotype a population of Braque Français, type Pyrénées dogs with the high-density SNP array to study the genomic diversity of the breed. Results The average observed (\docum…
Application of microsatellite markers as potential tools for traceability of Girgentana goat breed dairy products
2015
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…
Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep p…
2019
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…
Conservation status and historical relatedness of Italian cattle breeds
2018
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…
Association study between beta-defensin gene polymorphisms and mastitis resistance in Valle del Belice dairy sheep breed
2016
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 …
Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds
2018
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…
Study of polymorphisms in the promoter region of ovine β-lactoglobulin gene and phylogenetic analysis among the Valle del Belice breed and other shee…
2012
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…
Seven Shades of Grey: A Follow-Up Study on the Molecular Basis of Coat Colour in Indicine Grey Cattle Using Genome-Wide SNP Data
2022
Shades of grey and brown are a dominant component in mammal coat colours, representing a fundamental trait involved in a great number of processes including cryptism, sexual selection and signalling. The genetic mechanisms of the grey colouration in mammals are very complex and controlled by hundreds of genes whose effects and interactions are still largely unclear. In this study, we adopted a robust multi-cohort Fst outlier approach based on pairwise contrasts between seven grey indicine cattle breeds and both taurine and indicine non-grey cattle breeds in order to find genomic regions potentially related to the grey colouration. On the basis of three main drawn settings, built in order to…
Genome-wide analysis identifies potentially causative genes explaining the phenotypic variability in Pinzirita sheep
2019
Genome-wide analysis identifies potentially causative genes explaining the phenotypic variability in Pinzirita sheep
Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds
2020
The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). I…
The Girgentana Goat Breed: A Zootechnical Overview on Genetics, Nutrition and Dairy Production Aspects
2017
In recent years, there has been a great interest in recovering and preserving local livestock breeds. An interesting situation is represented by the Girgentana goat, an ancient local breed reared in Sicily. Over recent years, this breed has become almost extinct, in part as a consequence of the marked decrease in fresh goat milk consumption. On the basis of these considerations, several studies on its genetic structure and management aspects have been conducted in order to protect the Girgentana goat from the risk of extinction and recover its genetic and economic value. In this context, information on genetics, nutrition and dairy production aspects may have a crucial role in the improveme…
Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data
2020
Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomi…
Molecular characterisation of k-casein gene in Girgentana dairy goat breed and identification of two new alleles
2015
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
2013
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
2013
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 …
On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
2020
Background In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. Results We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of commo…
Additional file 10 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis…
2020
Additional file 10: Figure S6. Spatial PCA of 507 domestic sheep without EFB, KCH and VBS, which were found to dominate the sPC2 and sPC3 just as for in the normal PCA (Additional file 8: Figure S4 left panels). The three methods of triangulation, indicated above the plots, give essentially the same results, which are similar to the supervised PCA pattern (see Additional file 8: Figure S4 right panels).
MOESM13 of Conservation status and historical relatedness of Italian cattle breeds
2018
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.
2015
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
2017
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
2018
Additional file 6: Figure S3. Distribution of all ROH within breeds according to their size (kb).
Using of SNP markers to estimate inbreeding, coancestry and effective population size in Sicilian cattle breeds
2014
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 …
MOESM2 of Conservation status and historical relatedness of Italian cattle breeds
2018
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.
Loss in milk yield and related composition changes resulting from different levels of somatic cell count in Valle del Belice dairy sheep
2015
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…
Proteomics for milk proteins characterization in Girgentana goat breed
2013
Proteomics has been widely used to characterize milk protein content in livestock species and unravel protein biological functions. The aim of this work was to characterize the Girgentana goat breed whole milk and milk fraction proteins by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry. Bulk milk samples from two farms locate in Palermo and Agrigento (Sicily) areas were collected during the early stage of lactation. Initially, 2D-PAGE and protein detection protocols were set-up. In particular, 2D-PAGE analyses were carried out on whole milk using 18-cm IPG strips ranging from pH 3-10 and 4-7 and 12.5% polyacrylamide gel for first and the second dimension …
Two-dimensional difference in gel electrophoresis (2D-DIGE) for milk proteins characherization in Girgentana goat breed
2015
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…
MOESM3 of Conservation status and historical relatedness of Italian cattle breeds
2018
Additional file 3: Figure S1. Trends in historic effective population size (Ne) (from 13 to 98 generations).
Genetic diversity and phylogenetic relationships among four breeds reared in Sicily using β-lactoglobulin promoter region polymorphisms
2011
The aim of this work was to analyze the genetic diversity and the phylogenetic relationships among the Valle del Belice (VDB) breed and the other sheep breeds considered as ancestors, using -lactoglobulin (BLG) promoter region polymorphisms. The BLG promoter region of 50 randomly chosen animals from the four breeds (VDB n=20; Comisana (COM) n=10; Pinzirita (PIN) n=10; Sarda (SAR) n=10) were sequenced and aligned, and results showed the presence of 36 single nucleotide polymorphisms (SNPs) and one deletion. The number of polymorphic sites identified showed high variability within breeds. Nucleotide (π) and haplotype (Hd) diversity were estimated with DnaSP software, whereas PHASE software w…
QUANTIFICATION OF GENETIC VARIANTS OF CASEINS IN MILK OF GIRGENTANA GOAT BREED
2013
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 d…
2021
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).
Application of molecular markers to investigate genetic diversity in Sicilian livestock
2014
La diversità genetica delle specie e razze di interesse zootecnico, rappresenta un’importante risorsa in tutti i sistemi di allevamento . Per lo studio della diversità genetica, nel corso dei decenni sono stati sviluppati diversi metodi che si basano su informazioni del pedigree o su dati molecolari (microsatelliti e SNPs, Single Nucleotide Polymorphisms). Con l’aumento della disponibilità di marcatori molecolari per la maggior parte delle specie di interesse zootecnico, e con lo sviluppo di sofisticate tecniche analitiche, sta crescendo la capacità di caratterizzare la variabilità genetica delle razze. Inoltre, ad oggi, poche sono le informazioni sulla diversità genetica delle razze e dell…
MOESM1 of Conservation status and historical relatedness of Italian cattle breeds
2018
Additional file 1. Description of each Italian local cattle breed involved in this study [68].
Additional file 2 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
2021
Additional file 2: Figure S2. Manhattan plots representing the signals of signatures of selection in the two population groups (CSD and NRD), of the ��ROH, and averaged FST. CSD = Central-southern population group; NRD = Northern population group.
Additional file 11 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis…
2020
Additional file 11: Figure S7. Supervised PCA of 546 animals in which the PC (svPC1, svPC2) were calculated based on the indicated fat-tailed, Nordic and Spanish sheep.
Caratterizzazione genetica mediante microsatelliti di una popolazione caprina siciliana
2013
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
2013
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…
PRELIMINARY STUDY ON QUANTIFICATION OF aS1-CASEIN VARIANTS IN GIRGENTANA GOAT BREED BY DIRECT CHROMATOGRAPHIC ANALYSIS OF MILK
2012
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…
Genome-wide characterization of local cattle breeds from central and western Mediterranean
2017
Following-up on previous studies that investigated genetic relationships among several world-wide cattle breeds using genome-wide SNP data, we focus here on the central and western part of the Mediterranean. Notably, 50K genotypes from 30 Marismeña (Spain); 24 Guelmoise (Algeria); 46 Brune de l’Atlas Fauve, 15 Brune de l’Atlas Grise, and 15 Blonde du Cap (Tunisia); 29 Modicana and 30 Cinisara (Sicily); 24 Podolica Italiana (Southern continental Italy); 34 Chianina and 24 Romagnola (Central Italy); 23 Modenese, 24 Reggiana, 23 Alpine Grey and 50 Pezzata Rossa Italiana (Northern Italy); 50 Bruna Italiana and 50 Frisona Italiana were considered. When included in a world-wide dataset, the three…
Additional file 14 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis…
2020
Additional file 14: Figure S9. Neighbor-net graphs of 17 regional groups of breeds (Additional file 12 B) with (A) AMF, (B) EMF, (C, D) both AMF and EMF; (D, E) pattern obtained by increasing the AMF-EFM distance in order to suppress the EMF-AMF clustering and to show different affinities of EMF and AMF for European domestic sheep.
High-Density Genomic Characterization of Native Croatian Sheep Breeds
2022
A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analy…
ASSOCIATION BETWEEN THE POLYMORPHISM AT CASEIN LOCI AND MILK FATTY ACID COMPOSITION IN GIRGENTANA GOATS
2013
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
2013
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
2015
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
2017
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…
Additional file 6 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis …
2020
Additional file 6: Figure S2. Neighbour-joining tree visualizing the allele-sharing distances of the Balkan sheep (see Fig. 1) or (see Additional file 1: Table S1) for the breed codes). Breeds that are dispersed over different branches of the tree are indicated by colored lines.
Genome structure in Sicilian cattle breeds
2014
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…
Additional file 13 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis…
2020
Additional file 13: Figure S8. Neighbor-net graph of Reynolds’ distances between breeds or regional combinations of closely related breeds (see Additional file 12: Table S5).
Molecular characterization of the Sicilian goat populations
2014
The Sicilian goats are characterized by a strong population admixture structure, caused by geographical location of the farms, influences of natural mating and traditional breeding systems where flock represents an important breeding unit. Nowadays, several local populations are reared in Sicily, some of which do not have a recognized defined genetic structure, having taken origin from several crosses between animals of different breeds/populations sharing the same environment. The aim of this work was to characterize the Sicilian autochthonous goat populations using microsatellite markers and genetic polymorphisms of casein genes
MOESM10 of Conservation status and historical relatedness of Italian cattle breeds
2018
Additional file 10: Figure S6. Scatter plot of correlations between genetic differentiation (FST) and geographical distances for all breeds.
Genetic variability of Girgentana goat breed using molecular markers
2014
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 8 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis …
2020
Additional file 8: Figure S4. Left panels: normal PCA plots of 525 sheep (≤ 6 per breed) including the inbred EFB, KCH, VBS. Right panels: supervised PCA of 546 sheep, including three mouflon populations, in which EFB, KCH and VBS as well as the mouflons have been excluded for calculation of the principal components (svPC1, svPC2 and svPC3).
Additional file 16 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis…
2020
Additional file 16. Methodological comparisons and considerations [22, 50, 53, 54, 56, 64, 65, 77].
Additional file 3 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP da…
2021
Additional file 3: Table S2. Set of priors used to model the scenarios in the ABC framework.
MOESM4 of Conservation status and historical relatedness of Italian cattle breeds
2018
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>4Mb) and recent and historical Ne estimated 13 (Ne13), 20 (Ne_20 and 80 (Ne_80) generations ago. (* p- valueâ
Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of C…
2020
Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes. Using medium-density SNP array genotype data, a multi-cohort FST-outlier approach was adopted for a total of 60 pair-wise comparisons of the 15 grey with 4 non-grey cattle breeds (Angus, Limousin, Charolais, and Holstein), with the latter sel…
MOESM7 of Conservation status and historical relatedness of Italian cattle breeds
2018
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).
Additional file 4 of The genetic heritage of Alpine local cattle breeds using genomic SNP data
2020
Additional file 4: Table S2. Fixation indices (FST) between all pairs of breed populations analyzed in this study.
Genome-wide association study for milk production traits in Valle del Belice sheep
2017
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 …
Additional file 1 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP da…
2021
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.
Additional file 5 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis …
2020
Additional file 5: Figure S1. Inverse linear relationship of observed heterozygosity and the total ROH coverage FROH, showing relatively low heterozygosity values for AMF, SMF and fat-tailed sheep.
Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in local cattle breeds
2015
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…
MOESM1 of Genome-wide diversity and runs of homozygosity in the “Braque Français, type Pyrénées” dog breed
2018
Additional file 1. Plink command lines. File with the Plink command lines used to: (i) edite the SNP data; (ii) select unlinked SNP loci for the estimation of $$N_e$$ N e ; (iii) detect runs of homozygosity (ROH).
Additional file 1 of The genetic heritage of Alpine local cattle breeds using genomic SNP data
2020
Additional file 1: Table S1. Name of the breeds, sample size, breed codes and source of genotyping data.
Genome wide Copy Number Variation (CNV) detection in Cinisara cattle breed
2017
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
2017
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.
Additional file 9 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis …
2020
Additional file 9: Figure S5. Supervised PCA of 546 animals as in Fig. 2b, showing svPC1 vs. svPC3 averaged per breed.
The climatic and genetic heritage of Italian goat breeds with genomic SNP data
2021
Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including > 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo-political situation prec…
Italian Goat Consortium: a collaborative project to study the Italian caprine biodiversity.
2017
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
2015
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…
Genetic diversity of Mediterranean cattle breeds related to geography and climate
2015
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 15 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis…
2020
Additional file 15: Figure S10. TreeMix trees without and with 6, 10 and 20 migrations and plots of the proportions of the variance explained (f-indices) and likelihoods at different m values. Coloured lines indicate inferred migrations with a weight according to the color scale.
Additional file 1 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
2021
Additional file 1: Figure S1. Geographic distribution (a), phylogeny tree (b), and multidimensional scaling analysis (c) of all the Italian goat breeds included in the study.
Polymorphisms at β-defensin genes and mastitis in Valle del Belice dairy sheep: a case control study
2015
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…
Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds
2014
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
2017
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).
Additional file 7 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis …
2020
Additional file 7: Figure S3. FineStructure clustering of eastern and southeastern European sheep breeds. The color of each bin in the matrix indicates the number of “genomic chunks” copied from a donor (columns) to a recipient individual (rows).
Identification of breed informative single nucleotide polymorphisms for assigning individual in Sicilian dairy sheep
2015
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
2017
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 …
Linkage disequilibrium and genetic diversity estimation in three Sicilian autochthonous dairy sheep breeds
2014
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…
Genetic structure and assignment test in five sheep breeds reared in Sicily using microsatellites
2011
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…
MOESM1 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
2017
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.
MOESM8 of Conservation status and historical relatedness of Italian cattle breeds
2018
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
2015
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…
Genomic diversity and population structure analysis reveal few genetic differences among Ethiopian indigenous sheep populations
2017
African sheep, like other domestic sheep, are domesticated from the Asiatic mouflon (Ovis orientalis). They entered the continent through the North and the Horn of Africa regions following maritime and terrestrial trading routes. Ethiopia is one of the main entry points of various plant and animal domesticates into Africa. It is characterised by diverse agro-ecologies, ancient human ethnic diversity and the presence of indigenous sheep breeds/populations of unprecedented morphological diversity (e.g. tail types). Here, we investigate the genome diversity and population structure of 146 unrelated animals from 11 Ethiopian indigenous sheep populations. DNA was extracted from ear tissue punche…
MOESM4 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
2017
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.
MOESM12 of Conservation status and historical relatedness of Italian cattle breeds
2018
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
2017
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 8 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP da…
2021
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 da…
2021
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
2018
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 da…
2021
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 3 of The genetic heritage of Alpine local cattle breeds using genomic SNP data
2020
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
2020
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 da…
2021
Additional file 9: Figure S7. Principal component analysis (PCA) for the two datasets used (17 K and 8 K).
Additional file 3 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
2021
Additional file 3: Table S1. List of the genes identified by the analyses of the signatures of selection: top 1% homozygosity score in CSD and NRD groups, ��ROH, and averaged FST. CSD = Central-southern population group; NRD = Northern population group.
Additional file 2 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis …
2020
Additional file 2: Table S2. Datasets used for analysis.
Additional file 7 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP da…
2021
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 2 of The genetic heritage of Alpine local cattle breeds using genomic SNP data
2020
Additional file 2: Figure S1. Cross-validation plot of admixture analysis for all values of K (number of clusters) ranging from 2 to 28.
MOESM6 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
2017
Additional file 6: Table S2. List of 107 potential candidate genes under directional selection in the Valle del Belice sheep breed.
Variation of proteomic profile during lactation in Girgentana goat milk: a preliminary study
2018
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 1 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis …
2020
Additional file 1: Table S1. Sheep breeds analyzed in this study [16, 18, 20, 22, 31, 35, 47, 59, 76]. Colors indicate genetic clusters. Boxes indicate breeds combined in the 78-breed panel.
MOESM5 of Conservation status and historical relatedness of Italian cattle breeds
2018
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
2018
Additional file 9: Table S3. Pairwise FST values between cattle populations.
Additional file 3 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis …
2020
Additional file 3: Table S3. A 358 SNPs informative for Asian Mouflon ancestry used in BSAA. Only SNPs were considered with > 40 out of 42, > 55 out of 57 and > 67 out of 69 non-missing allele frequencies used for the pairwise AFM-PRMS, AMF-EMFM and EMFM-PRMS FST calculations, respectively. B 334 SNPs informative for Asian Mouflon ancestry used in BSAA. Only SNPs were considered with > 67 out of 69, > 55 out of 57 and > 40 out of 42 non-missing allele frequencies used for the pairwise EMFM-PRMS, AMF-EMFM and AFM-PRMS FST calculations, respectively. C 606 SNPs informative for Merino ancestry used in BSAA. Only SNPs were considered without missing allele frequencies used for…
Additional file 6 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP da…
2021
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 12 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis…
2020
Additional file 12: Table S5. Grouping of breeds for calculation of genetic distances. (A) Regional monophyletic groups of breeds for the Neighbor-net graph in Additional file 13: Figure S8. (B) 17 Regional groups of related breeds for the Neighbor-net graphs in Fig. 3 and Additional file 14: Figure S9.
Additional file 4 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis …
2020
Additional file 4: Table S4. ROH statistic per individual or averaged per breed. FROH is the total length of the ROH divided by the total length of the sheep autosomes (2452.06 Mb).
Additional file 4 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP da…
2021
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).