BackgroundPortugal and Spain, with six and 22 officially recognized caprine breeds, encompass 25 % of the European Union goat census. Many of these populations have suffered strong demographic declines because of competition with exotic breeds and the phasing-out of low income rural activities. In this study, we have investigated the consequences of these and other demographic processes on the genetic diversity, population structure and inbreeding levels of Iberian and Atlantic goats.MethodsA sample of 975 individuals representing 25 officially recognized breeds from Portugal and Spain, two small populations not officially recognized (Formentera and Ajuí goats) and two ecotypes of the Tinerfeña and Blanca Celtibérica breeds were genotyped with a panel of 20 microsatellite markers. A wide array of population genetics methods was applied to make inferences about the genetic relationships and demography of these caprine populations.ResultsGenetic differentiation among Portuguese and Spanish breeds was weak but significant (FST = 0.07; P < 0.001), which is probably the consequence of their short splitting times and extensive gene flow due to transhumance. In contrast, Canarian goats were strongly differentiated because of prolonged geographic isolation. Most populations displayed considerable levels of diversity (mean He = 0.65).ConclusionsHigh diversity levels and weak population structures are distinctive features of Portuguese and Spanish breeds. In general, these local breeds have a reduced census, but are still important reservoirs of genetic diversity. These findings reinforce the need for the implementation of management and breeding programs based on genetic data in order to minimize inbreeding, maintain overall genetic and allelic diversities and breed identities, while at the same time taking into account the within-breed genetic structure.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0167-8) contains supplementary material, which is available to authorized users.

In this study, we genetically characterized the Uruguayan pig breed Pampa Rocha. Genetic variability was assessed by analyzing a panel of 25 microsatellite markers from a sample of 39 individuals. Pampa Rocha pigs showed high genetic variability with observed and expected heterozygosities of 0.583 and 0.603, respectively. The mean number of alleles was 5.72. Twenty-four markers were polymorphic, with 95.8% of them in Hardy Weinberg equilibrium. The level of endogamy was low (FIS = 0.0475). A factorial analysis of correspondence was used to assess the genetic differences between Pampa Rocha and other pig breeds; genetic distances were calculated, and a tree was designed to reflect the distance matrix. Individuals were also allocated into clusters. This analysis showed that the Pampa Rocha breed was separated from the other breeds along the first and second axes. The neighbour-joining tree generated by the genetic distances DA showed clustering of Pampa Rocha with the Meishan breed. The allocation of individuals to clusters showed a clear separation of Pampa Rocha pigs. These results provide insights into the genetic variability of Pampa Rocha pigs and indicate that this breed is a well-defined genetic entity.

The objective of the present study was to assess the frequency distribution of markers in the diacylglycerol acyltransferase (DGAT1), fatty acid binding protein 4 (FABP4), leptin (LEP), retinoic acid receptor-related orphan receptor C (RORC), and stearoyl-CoA desaturase (SCD1) genes in a Spanish commercial crossbred population (n = 286) produced in southwest Spain. We have also evaluated the association of these 5 major SNP with backfat thickness (BFT) and intramuscular fat (IMF) to use them routinely in the industry (if the associations are confirmed) due to their ease of use. The KK genotype of the DGAT1 gene was associated (P = 0.046) with the greatest BFT value. Bulls presenting the GG genotype for SNP in the FABP4 gene showed greater values for the percentage of IMF (P = 0.030), which means an increase of 0.155% IMF per copy of the G allele of this marker (P = 0.009). A significant association was found between the RORC: g.3290T > G marker and the percentage of IMF. The GG genotype of the RORC: g.3290T > G marker showed the lowest IMF percentage (P = 0.025). The specific associations found in this study not only provide information about the involvement of these genes in the fat deposition at different levels in the southwestern Spain cattle population, but can also serve as a tool to improve certain meat quality attributes through Marker Assisted Selection. However, sensory studies are needed to explore further the usefulness of these genes in meat quality and the impact on the actual palatability of the beef.

No abstract

Background: In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions. Results: Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 Bead-Chip, we were able to detect 4617 and 7750 autosomal CNV with the PennCNV and QuantiSNP software, respectively. By applying the EnsembleCNV algorithm, these CNV were assembled into 1461 CNV regions (CNVR), of which 486 (33.3% of the total CNVR count) were consistently called by PennCNV and QuantiSNP and used in subsequent analyses. In this set of 486 CNVR, we identified 78 gain, 353 loss and 55 gain/loss events. The total length of all the CNVR (95.69 Mb) represented 3.9% of the goat autosomal genome (2466.19 Mb), whereas their size ranged from 2.0 kb to 11.1 Mb, with an average size of 196.89 kb. Functional annotation of the genes that overlapped with the CNVR revealed an enrichment of pathways related with olfactory transduction (fold-enrichment = 2.33, q-value = 1.61 × 10 −10), ABC transporters (fold-enrichment = 5.27, q-value = 4.27 × 10 −04) and bile secretion (foldenrichment = 3.90, q-value = 5.70 × 10 −03). Conclusions: A previous study reported that the average number of CNVR per goat breed was ~ 20 (978 CNVR/50 breeds), which is much smaller than the number we found here (486 CNVR). We attribute this difference to the fact that the previous study included multiple caprine breeds that were represented by small to moderate numbers of individuals. Given the low frequencies of CNV (in our study, the average frequency of CNV is 1.44%), such a design would probably underestimate the levels of the diversity of CNV at the within-breed level. We also observed that functions related with sensory perception, metabolism and embryo development are overrepresented in the set of genes that overlapped with CNV, and that these loci often belong to large multigene families with tens, hundreds or thousands of paralogous members, a feature that could favor the occurrence of duplications or deletions by nonallelic homologous recombination.