0000000000940887
AUTHOR
Fabio Pilla
MOESM13 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 13: Figure S7. Genetic relationship defined with multidimensional scaling analysis between Italian and 62 European cattle breeds. The breeds were grouped according to their geographical origins and distributions. Northern_Europe (Belgian Blue, Dexter, Kerry, Lithuanian Light Grey, Lithuanian White Backed, Groningen Whitehead, Lakenvelder, Meuse-Rhine-Ijjsel, Norwegian Red, Finnish Ayrshire, Belted Galloway, Galloway, Angus, Scottish Highland, South Devon), England (Devon, Guernsey, Hereford, Longhorn, Lincoln Red, Milking Shorthorn, Red Poll, Beef Shorthorn, Sussex, Welsh Blach, White Park), Spain (Berrenda en Negro, Berrenda en Colorado, Cardena Andaluza, Menorquina, Pirena…
MOESM6 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 6: Figure S3. Distribution of all ROH within breeds according to their size (kb).
Genome-wide scan of fat-tail sheep identifies signals of selection for fat deposition and adaptation
Fat tail in sheep represents a valuable energy reserve for facing future climate changes. The identification of genes with a role in the fat-tail phenotype may contribute to understanding the physiology of fat deposition and the mechanisms of adaptation. Genotypic data obtained with the OvineSNP50K array in 13 thin-tail sheep breeds from Italy were used to identify selection signatures of fat tail through pairwise thin- versus fat-tail sheep breed comparisons, with the following fat-tail breeds of the Mediterranean area: two unique Italian fat-tail breeds (Barbaresca and Laticauda), a Barbary sheep breed from Libya, Ossimi breed from Egypt, Cyprus Fat-Tail and Chios from the Greek islands …
Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
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…
How Geography and Climate Shaped the Genomic Diversity of Italian Local Cattle and Sheep Breeds
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…
Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia
International audience; Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging to 23 sheep breeds of different geographic origins using the Rsb (extended haplotype homozygosity) and FST statistical approaches, to identify loci associated with the fat-tail phenotype. We also checked if these putative selection signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel signals and confirmed the presence of selection signature in genomic regio…
MOESM2 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 2: Table S1. Name of the breeds, geographic coordinates (longitude and latitude) of the center of origin, sample size before (n-PreQC) and after (n-PostQC) genotyping quality control, and origin of genotyping data.
Genome-wide detection of signatures of selection in three Valdostana cattle populations
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…
MOESM3 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 3: Figure S1. Trends in historic effective population size (Ne) (from 13 to 98 generations).
Genome-wide assessment of diversity and differentiation between original and modern Brown cattle populations
Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity (ROH) islands using the Illumina Bovine SNP50 BeadChip genotyping data. After quality control, 34 735 SNPs and 106 animals were retained for the analyses. Larger heterogeneity was highlighted for the original populations. Patterns of genetic differentiation, multidimensional scaling, and the neig…
Additional file 10 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 10: Figure S8. Projection on a single LDA axis in the model-grouping approach (a) and on the first two LDA axes in the six scenarios separately (b).
MOESM1 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 1. Description of each Italian local cattle breed involved in this study [68].
Additional file 2 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
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.
Genome-wide variation, candidate regions and genes associated with fat deposition and tail morphology in Ethiopian indigenous sheep
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 diversity of Pagliarola sheep residual population and its conservation implication
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…
MOESM10 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 10: Figure S6. Scatter plot of correlations between genetic differentiation (FST) and geographical distances for all breeds.
On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
AbstractBackgroundDuring the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, throug…
Additional file 3 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 3: Table S2. Set of priors used to model the scenarios in the ABC framework.
MOESM4 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 4: Table S2. Pearson correlation coefficients between genetic diversity indices. Observed (Ho) and expected (He) heterozygosity, average minor allele frequency (MAF), inbreeding coefficient (FHOM), contemporary effective population size (cNe), mean ROH-based inbreeding coefficient (FROH>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 Coat Color
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
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
Additional file 4: Table S2. Fixation indices (FST) between all pairs of breed populations analyzed in this study.
Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations.
Selective breeding has led to modifications in the genome of many livestock breeds. In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case–control genome-wide association study (GWAS), the Bayesian population differentiation analysis (FST) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and FST and one marker bet…
Additional file 1 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 1: Table S1. Name of the breeds, breed codes, sample size (N), sub-species, continent and geographic origin, and source of genotyping data.
Conservation status and historical relatedness of Italian cattle breeds
Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Ou…
Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds
The availability of dense single nucleotide polymorphism (SNP) assays allows for the determination of autozygous segments based on runs of consecutive homozygous genotypes (ROH). The aim of the present study was to investigate the occurrence and distribution of ROH in 21 Italian sheep breeds using medium-density SNP genotypes in order to characterize autozygosity and identify genomic regions that frequently appeared in ROH within individuals, namely ROH islands. After filtering, the final number of animals and SNPs retained for analyses were 502 and 46 277 respectively. A total of 12 302 ROH were identified. The mean number of ROH per breed ranged from 10.58 (Comisana) to 44.54 (Valle del B…
Additional file 1 of The genetic heritage of Alpine local cattle breeds using genomic SNP data
Additional file 1: Table S1. Name of the breeds, sample size, breed codes and source of genotyping data.
The genetic heritage of Alpine local cattle breeds using genomic SNP data
Abstract Background Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc an…
The climatic and genetic heritage of Italian goat breeds with genomic SNP data
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…
Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle
AbstractThe availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide. However, these comprehensive studies did not include some local European populations, including autochthonous Italian cattle. In this study, we assembled a large-scale, genome-wide dataset of single nucleotide polymorphisms scored in 3,283 individuals from 205 cattle populations worldwide to assess genome-wide autozygosity and understand better the genetic relationships among these populations. We prioritized European cattle, with a special focus on Italian breeds. Moderate differences in estimates of molecular inbreeding calculated from runs of homozygosity (FROH) were o…
Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle
The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses …
Seven Shades of Grey: A Follow-Up Study on the Molecular Basis of Coat Colour in Indicine Grey Cattle Using Genome-Wide SNP Data
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 of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds
Summary Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north–south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sa…
Additional file 1 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
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.
Analysis of runs of homozygosity of cattle living in different climate zones
Abstract Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds’ country of…
A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds
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…
MOESM8 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 8: Figure S5. Cross-validation errors of admixture analysis at different K values.
MOESM12 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 12: Table S5. Results of the f4 test.
Additional file 8 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 8: Figure S6. Increment in the log likelihood for the reduced (European taurine and the Guelmoise) dataset for all tested migration events, calculated by using the optM function in the R package OptM.
Additional file 5 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 5: Figure S3. Cross-validation plot of the admixture analysis for all values of K (number of clusters) ranging from 2 to 23.
MOESM11 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 11: Table S4. Results of the f3 test.
Additional file 2 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 2: Figure S1. All modelled scenarios for colonization tested in the ABC framework. Description: In all the tested scenarios, we assumed that taurine and indicine cattle separated first. Subsequent reduction in effective population size was modelled to take the two independent domestication events that occurred in the Fertile Crescent and the Indus Valley into account. From these known evolutionary events, two sets of scenarios were built. The first three scenarios mirror to two different waves of migration, an early Neolithic migration involving non-Podolian taurine cattle and a secondary migration involving Podolian cattle after their genetic admixture with indicine cattle …
Additional file 3 of The genetic heritage of Alpine local cattle breeds using genomic SNP data
Additional file 3: Figure S2. Admixture analysis plot in a circular fashion with all values of K (number of clusters) ranging from 2 to 28.
Additional file 5 of The genetic heritage of Alpine local cattle breeds using genomic SNP data
Additional file 5: Figure S3. Increment in the log likelihood for all tested migration events calculated by using the optM function in the R package OptM.
Additional file 9 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 9: Figure S7. Principal component analysis (PCA) for the two datasets used (17 K and 8 K).
Additional file 3 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
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 7 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 7: Figure S5. Increment in the log likelihood for the complete dataset for all tested migration events, calculated by using the optM function in the R package OptM.
Additional file 2 of The genetic heritage of Alpine local cattle breeds using genomic SNP data
Additional file 2: Figure S1. Cross-validation plot of admixture analysis for all values of K (number of clusters) ranging from 2 to 28.
MOESM5 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 5: Figure S2. Relationship between the number of ROH and the length of the genome (Mb) covered by ROH per individual.
MOESM9 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 9: Table S3. Pairwise FST values between cattle populations.
Additional file 6 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 6: Figure S4. Admixture analysis plot in a circular fashion with all values of K (number of clusters) ranging from 2 to 23.
Additional file 4 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 4: Figure S2. Genetic diversity indices: observed and expected heterozygosity (Ho and He), effective population size (Ne) and minor allele frequencies (MAF) calculated for each breed. Asian indicine (blue), African taurine (yellow), European Podolian (orange), European non-Podolian (red).