Browsing by Author "Borges, Carla"
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- Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) PopulationPublication . Mendes, Bruna; Sampaio, Teresa; Antunes, Marta A.; Magalhães, Hugo; Silva, Filipe Costa; Borges, Carla; Simões, Fernanda; Usié, Ana; Almeida, Maria Helena; Ramos, António MarcosCork oak (Quercus suber L.) is a valuable forest species in the western Mediterranean Basin due to its ecological value and the production of cork (a renewable natural material). Cork quality depends on the genetic background and cork oak environment, which has long been recognized. As no cork oak genetic trials with pedigree information were available, the inference of the genetic relatedness between individuals from molecular markers can potentially be applied to natural populations. This work aimed to investigate the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping a natural cork oak population. A total of 494 trees located in Portugal were genotyped with 8K SNPs. The raw SNP set was filtered differently, producing four SNP sets that were further filtered by missing data, genotype frequency, and minor allele frequency. For each set, an identity by descent (IBD) matrix was generated to perform the relationship prediction, revealing from 22,114 to 23,859 relationships. Familial categories from the first to the third degree were able to be assigned. The feasibility of SNP genotyping for future studies on the kinship analysis and pedigree reconstruction of cork oak populations was demonstrated. The information produced may be used in further breeding and conservation programs for cork oak
- Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) PopulationPublication . Mendes, Bruna; Sampaio, Teresa; Antunes, Marta; Magalhães, Hugo; Costa e Silva, Filipe; Borges, Carla; Simões, Fernanda; Usié, Ana; Almeida, Maria Helena; Ramos, António MarcosCork oak (Quercus suber L.) is a valuable forest species in the western Mediterranean Basin due to its ecological value and the production of cork (a renewable natural material). Cork quality depends on the genetic background and cork oak environment, which has long been recognized. As no cork oak genetic trials with pedigree information were available, the inference of the genetic relatedness between individuals from molecular markers can potentially be applied to natural populations. This work aimed to investigate the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping a natural cork oak population. A total of 494 trees located in Portugal were genotyped with 8K SNPs. The raw SNP set was filtered differently, producing four SNP sets that were further filtered by missing data, genotype frequency, and minor allele frequency. For each set, an identity by descent (IBD) matrix was generated to perform the relationship prediction, revealing from 22,114 to 23,859 relationships. Familial categories from the first to the third degree were able to be assigned. The feasibility of SNP genotyping for future studies on the kinship analysis and pedigree reconstruction of cork oak populations was demonstrated. The information produced may be used in further breeding and conservation programs for cork oak.
- New insights into the genetic composition and phylogenetic relationship of wolves and dogs in the Iberian PeninsulaPublication . Pires, Ana Elisabete; Amorim, Isabel R.; Borges, Carla; Simões, Fernanda; Teixeira, Tatiana; Quaresma, Andreia; Petrucci-Fonseca, Francisco; Matos, JoséThis study investigates the gene pool of Portuguese autochthonous dog breeds and their wild counterpart, the Iberian wolf subspecies (Canis lupus signatus), using standard molecular markers. A combination of paternal and maternal molecular markers was used to investigate the genetic composition, genetic differentiation and genetic relationship of native Portuguese dogs and the Iberian wolf. A total of 196 unrelated dogs, including breed and village dogs from Portugal, and other dogs from Spain and North Africa, and 56 Iberian wolves (wild and captive) were analyzed for nuclear markers, namely Y chromosome SNPs, Y chromosome STR loci, autosomal STR loci, and a mitochondrial fragment of the control region I. Our data reveal new variants for the molecular markers and confirm significant genetic differentiation between Iberian wolf and native domestic dogs from Portugal. Based on our sampling, no signs of recent introgression between the two subspecies were detected. Y chromosome data do not reveal genetic differentiation among the analyzed dog breeds, suggesting they share the same patrilineal origin. Moreover, the genetic distinctiveness of the Iberian wolf from other wolf populations is further confirmed with the description of new mtDNA variants for this endemism. Our research also discloses new molecular markers for wolf and dog subspecies assignment, which might become particularly relevant in the case of forensic or noninvasive genetic studies. The Iberian wolf represents a relic of the once widespread wolf population in Europe and our study reveals that it is a reservoir of unique genetic diversity of the grey wolf, Canis lupus. These results stress the need for conservation plans that will guarantee the sustainability of this threatened top predator in Iberia.