0000000000725741
AUTHOR
Sara Casu
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.
A genomic map of climate adaptation in Mediterranean cattle breeds
International audience; Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate sub-types. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional…
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].
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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
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).
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…
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…
Genetic diversity of Mediterranean cattle breeds related to geography and climate
In recent decades, changes in climate have caused impacts on natural and human systems. Mediterranean countries will be particularly affected by this phenomenon, with growing temperatures and reduced rainfall. Understanding how species and ecosystems respond to climate change has become a crucial focus in biodiversity conservation and management. The genome-wide SNP panels allows providing background information on genome structure in domestic animals, opening new perspectives to livestock genetics. The International Project GALIMED "Genetic Adaptation of Bovine Livestock and production systems in MEDiterranean region", develops an integrated approach that combines the analysis of SNP marke…
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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.