Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Abstract Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italia…

Additional file 10 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 10: Figure S8. Projection on a single LDA axis in the model-grouping approach (a) and on the first two LDA axes in the six scenarios separately (b).

Additional file 2 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Additional file 2: Figure S2. Manhattan plots representing the signals of signatures of selection in the two population groups (CSD and NRD), of the ��ROH, and averaged FST. CSD = Central-southern population group; NRD = Northern population group.

Additional file 3 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 3: Table S2. Set of priors used to model the scenarios in the ABC framework.

BOVITA: a first overview on genome-wide genetic diversity of Italian autochthonous cattle breeds

Additional file 1 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 1: Table S1. Name of the breeds, breed codes, sample size (N), sub-species, continent and geographic origin, and source of genotyping data.

The climatic and genetic heritage of Italian goat breeds with genomic SNP data

Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including > 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo-political situation prec…

Additional file 1 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Additional file 1: Figure S1. Geographic distribution (a), phylogeny tree (b), and multidimensional scaling analysis (c) of all the Italian goat breeds included in the study.

Additional file 8 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 8: Figure S6. Increment in the log likelihood for the reduced (European taurine and the Guelmoise) dataset for all tested migration events, calculated by using the optM function in the R package OptM.

Additional file 5 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 5: Figure S3. Cross-validation plot of the admixture analysis for all values of K (number of clusters) ranging from 2 to 23.

Additional file 2 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 2: Figure S1. All modelled scenarios for colonization tested in the ABC framework. Description: In all the tested scenarios, we assumed that taurine and indicine cattle separated first. Subsequent reduction in effective population size was modelled to take the two independent domestication events that occurred in the Fertile Crescent and the Indus Valley into account. From these known evolutionary events, two sets of scenarios were built. The first three scenarios mirror to two different waves of migration, an early Neolithic migration involving non-Podolian taurine cattle and a secondary migration involving Podolian cattle after their genetic admixture with indicine cattle …

Additional file 9 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 9: Figure S7. Principal component analysis (PCA) for the two datasets used (17 K and 8 K).

Additional file 3 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Additional file 3: Table S1. List of the genes identified by the analyses of the signatures of selection: top 1% homozygosity score in CSD and NRD groups, ��ROH, and averaged FST. CSD = Central-southern population group; NRD = Northern population group.

Additional file 7 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 7: Figure S5. Increment in the log likelihood for the complete dataset for all tested migration events, calculated by using the optM function in the R package OptM.

Additional file 6 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 6: Figure S4. Admixture analysis plot in a circular fashion with all values of K (number of clusters) ranging from 2 to 23.

Additional file 4 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Additional file 4: Figure S2. Genetic diversity indices: observed and expected heterozygosity (Ho and He), effective population size (Ne) and minor allele frequencies (MAF) calculated for each breed. Asian indicine (blue), African taurine (yellow), European Podolian (orange), European non-Podolian (red).