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…

MOESM6 of Conservation status and historical relatedness of Italian cattle breeds

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

MOESM2 of Conservation status and historical relatedness of Italian cattle breeds

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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

2018

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

2018

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

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…

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…

Variance component estimation for SCS in different local breeds and species

2009

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.

MOESM4 of Conservation status and historical relatedness of Italian cattle breeds

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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

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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.

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.

MOESM8 of Conservation status and historical relatedness of Italian cattle breeds

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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

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

MOESM11 of Conservation status and historical relatedness of Italian cattle breeds

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

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 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.

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

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