0000000000164234
AUTHOR
Mariasilvia Dâandrea
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Additional file 6: Figure S3. Distribution of all ROH within breeds according to their size (kb).
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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.
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Additional file 3: Figure S1. Trends in historic effective population size (Ne) (from 13 to 98 generations).
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Additional file 1. Description of each Italian local cattle breed involved in this study [68].
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Additional file 10: Figure S6. Scatter plot of correlations between genetic differentiation (FST) and geographical distances for all 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
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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).
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Additional file 8: Figure S5. Cross-validation errors of admixture analysis at different K values.
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Additional file 12: Table S5. Results of the f4 test.
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Additional file 11: Table S4. Results of the f3 test.
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Additional file 5: Figure S2. Relationship between the number of ROH and the length of the genome (Mb) covered by ROH per individual.
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Additional file 9: Table S3. Pairwise FST values between cattle populations.