0000000000135106
AUTHOR
Rosalia Gerlando
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…
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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.