0000000000725746
AUTHOR
Donato Matassino
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).
A melanocortin 1 receptor (MC1R) gene polymorphism is useful for authentication of Massese sheep dairy products
Massese is an Italian sheep breed, with black or grey coat colour, mainly reared in the Tuscany and Emilia Romagna regions. Recently, the emerging interests in this breed have resulted in the production of Pecorino cheese obtained with only Massese milk. In order to be profitable, this marketing link between Massese breed and its products should be defended against fraudsters who could include milk of other sheep breeds or cow milk in Massese labelled productions. To identify the genetic factors affecting coat colour in sheep, we have recently analysed the melanocortin 1 receptor (MC1R) gene and identified several single nucleotide polymorphisms (SNPs). In this work, as a first step to set …
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.
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).
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].
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.
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
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).
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…
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…
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.
A first comparative map of copy number variations in the sheep genome.
article i nfo We carried out a cross species cattle-sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in cattle a…
MOESM12 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 12: Table S5. Results of the f4 test.
MOESM11 of Conservation status and historical relatedness of Italian cattle breeds
Additional file 11: Table S4. Results of the f3 test.
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.