Genotype data from 30 microsatellites were used to assess genetic diversity and relationships among 10 native Portuguese cattle breeds, American Charolais and the Brazilian Caracú. Hardy-Weinberg equilibrium was observed for all loci/population combinations except for five loci in Brava de Lide and one locus in Alentejana that exhibited heterozygote deficiency. Estimates of average observed and expected heterozygosities, total number of alleles (TNA) per breed and mean number of alleles (MNA) per locus/population were obtained. A total of 390 alleles were detected. TNA among Iberian cattle ranged from 170 to 237 and MNA ranged from 5.67 to 8.07. The highest observed heterozygosities were found in the Caracú, Maronesa, Garvonesa and Arouquesa and the lowest in Brava de Lide and Mirandesa. Estimation of population subdivision using Wright's FST index showed that the average proportion of genetic variation explained by breed differences was 9%. Neighbour-joining phylogenetic trees based on DA distances showed that the genetic relationships of present-day Portuguese native breeds are consistent with historical origins in the Brown Concave (Arouquesa, Mirandesa, Marinhoa) and Red Convex (Mertolenga, Alentejana, Garvonesa, Minhota) evolutionary groups. The Iberian Black Orthoide group, represented by Brava de Lide and Maronesa, and the Barrosã breed appeared to be more closely related to the Brown Concave group but may represent a separate lineage. The Caracú breed was not found to be closely associated with any of the native Portuguese breeds.

The quantitative assessment of genetic diversity within and between populations is important for decision-making in genetic conservation plans. In our study, we applied the livestock core set method to define the contribution of 15 cattle breeds, 11 of which are Portuguese indigenous cattle breeds, to genetic diversity. In livestock core set theory genetic diversity is defined as the maximum genetic variance that can be obtained in a random-mating population that is bred from the populations present in that core set. Two methods to estimate marker-estimated kinships to obtain the contributions to the core set were used in this study: the weighted log-linear model (WLM) and the weighted log-linear mixed model (WLMM). The breeds that contributed most to diversity in the core set were Holstein-Friesian followed by the Portuguese Mertolenga and Cachena for both WLM and WLMM methods. The ranking of relative contributions of cattle breeds was maintained when we considered only the Portuguese cattle breeds. Furthermore, we were able to identify the marginal contributions and respective losses of diversity for each of the 11 Portuguese cattle breeds when we considered a subset of populations that are not threatened of being lost (the Safe set composed of the four exotic breeds present in this study). When WLM was used losses in genetic diversity ranged from 2.68 to 0.65% while the loss in founder genome equivalents ranged from 37.37 to 8.43% for Mertolenga and Brava de Lide breeds respectively. When WLMM was used losses in genetic diversity and founder genome equivalents were less extreme than for the WLM method, ranging from 1.27 to 0.69 and 26.8 to 12.99 respectively.

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The genetic structure and diversity of nine ganadarias (the Portuguese word for bull farmer) of the Portuguese "Brava de Lide" (Bullfighting) breed were assessed with 30 microsatellites. Allelic richness per locus was low, with an overall average of 2 547. The mean number of alleles corrected for the size of the smaller sample ranged between 2,4 in ganadaria Jorge Mendes and 1,9 in ganadaria Vaz Monteiro. The mean expected and observed heterozygosities ranged between 0.627 in ganadaria Palha and 0.461 in ganadaria Vaz Monteiro and between 0.617 in ganadaria Cabral D'Ascension and 0.4485 in ganadaria Vaz Monteiro, respectively. The ganadaria Vaz Monteiro was the one that systematically showed the lowest values of genetic diversity. To analyse the substructure among the 51 animals studied, a factorial correspondence analysis and a Bayesian approach were performed using the Genetix and STRUCTURE programs, respectively.

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