ORCID Profile
0000-0003-2278-7089
Current Organisations
Universidade do Porto
,
Universidade do Porto Faculdade de Ciências
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Publisher: Frontiers Media SA
Date: 04-03-2015
Publisher: Springer Science and Business Media LLC
Date: 15-08-2023
DOI: 10.1186/S13059-023-03023-7
Abstract: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 in iduals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. We report the analysis of 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 s led breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
Publisher: Public Library of Science (PLoS)
Date: 06-01-2011
Publisher: MDPI AG
Date: 09-11-2011
DOI: 10.3390/D3040660
Abstract: Classification of cattle breeds contributes to our understanding of the history of cattle and is essential for an effective conservation of genetic ersity. Here we review the various classifications over the last two centuries and compare the most recent classifications with genetic data. The classifications devised during the 19th to the late 20th century were in line with the Linnaean taxonomy and emphasized cranial or horn morphology. Subsequent classifications were based on coat color, geographic origin or molecular markers. Several theories were developed that linked breed characteristics either to a supposed ancestral aurochs subspecies or to a presumed ethnic origin. Most of the older classifications have now been discarded, but have introduced several Latin terms that are still in use. The most consistent classification was proposed in 1995 by Felius and emphasizes the geographic origin of breeds. This is largely in agreement with the breed clusters indicated by a biochemical and molecular genetic analysis, which reflect either groups of breeds with a common geographic origin or single breeds that have expanded by export and/or crossbreeding. We propose that this information is also relevant for managing the genetic ersity of cattle.
Location: Portugal
Location: Portugal
Location: Portugal
No related grants have been discovered for Catarina Ginja.