Intrabreed Stratification Related to Divergent Selection Regimes in Purebred Dogs May Affect the Interpretation of Genetic Association Studies

Population Subdivision and Migration Assessment of Mangalica Pig Breeds Based on Pedigree Analysis

In conserving the genetic diversity of domestic animal breeds, strategies that emphasise between-breed diversity may not be optimal, as they neglect within-breed variation. The aim of the present study was to assess the extent of population subdivision in three Mangalica pig breeds and the contribution of migration to their substructure. Wright's FST coefficient was calculated based on genealogical data with breeding animals born between 1981 and 2023, with three colour variants (Blonde, Swallow-Belly and Red). These Wright's FST coefficients were analysed using multidimensional scaling to reveal the population substructure. The average FST coefficient was 0.04 for the Blonde breed and 0.047 for the Swallow-Belly and Red Mangalica breeds, while these parameters were lower in the active herds at 0.03 and 0.04, respectively. The migration of individuals between herds was 61.63% for the Blonde breed and 75.53% and 63.64% for the Swallow-Belly and Red Magalica breeds, respectively. No population substructure was observed in any of the Mangalica breeds, which can be explained by the extensive migration between herds.

Intra- and interbreed genetic heterogeneity and divergence in four commercial pig breeds based on microsatellite markers

In recent years, there has been an increasing amount of attention paid to the genetic health of domesticated animals and its relationship with the level of inbreeding and genetic diversity. At the same time, insufficient attention is still paid to the study of intrabreed genetic diversity and intrabreed stratification. The main goal of our work was to analyze the intra- and interbreed genetic diversity of commercial pig breeds on the basis of DNA microsatellite (MS-DNA) polymorphism. In total, the work used data for 3,308 pigs, which represented 11 herds. The animals belonged to four commercial pig breeds – Duroc (DR), Yorkshire (YR), Landrace (LN) and Large White (LW). 12 microsatellite loci recommended by ISAG-FAO and arranged in one multiplex panel (S0101, S0155, S0228, S0355, S0386, SW24, SW240, SW72, SW857, SW911, SW936, SW951) were used as DNA markers. When analyzing the intra- and interbreed variability of 11 herds, we found that all studied breeds significantly differed in terms of the proportion of both rare and the most common alleles. At the same time, the noted differences were determined, first of all, by the variability between individual herds within their breed. The location of herd centroids is random and is not consistent with their breed affiliation at all. When individuals belonging to the same breed are combined, the centroids of pig breeds in the space of first two axes from a Principal Coordinate Analysis form two clusters. The first one contains the only red pig breed (DR) used in the analysis, while the second one contains white pig breeds. In six pig herds the Ne estimates were below 50 inds., in two herds they were in the range of 50–100 inds., and finally in three herds the Ne estimates exceeded 100 inds. The analysis of the genetic variability of pigs of four commercial breeds showed that the high level of interbreed differences is caused, first of all, by the high variability among pig herds within each studied breed. Such intrabreed stratification can be formed due to the manifestation of many causes: different genetic basis of the founders of intrabreed genealogical groups, geographical isolation, different directions of selection within individual herds, exchange of animals between separate herds, the use of inbreeding in the practice of selection together with isolation, etc. Important consequences of intrabreed stratification are an increase in the level of interherd diversity (which is not lower than the level of interbreed diversity) against the background of a decrease in variability within individual herds, as well as a significant deficit of heterozygotes and an increase in the role of negative genetic and demographic processes. Thus, the existence of genetic heterogeneity within commercial pig breeds should be considered as an essential element in the history of their formation and breeding.

Genomic data illuminates demography, genetic structure and selection of a popular dog breed

BACKGROUND

Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever.

RESULTS

We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and also with coat colour (i.e. black, yellow, brown). There was little evidence of geographical differentiation. Highly differentiated genomic regions contained genes and markers associated with skull shape, suggesting that at least some of the differentiation is related to human-imposed selection on this trait. We also found that the total length of homozygous segments (runs of homozygosity, ROHs) was highly correlated with inbreeding coefficient.

CONCLUSIONS

This study demonstrates that high-density genomic data can be used to quantify genetic diversity and to decipher demographic and selection processes. Analysis of genetically differentiated regions in the UK Labrador Retriever population suggests the possibility of human-imposed selection on craniofacial characteristics. The high correlation between estimates of inbreeding from genomic and pedigree data for this breed demonstrates that genomic approaches can be used to quantify inbreeding levels in dogs, which will be particularly useful where pedigree information is missing.

Similar recent selection criteria associated with different behavioural effects in two dog breeds

Selection during the last decades has split some established dog breeds into morphologically and behaviourally divergent types. These breed splits are interesting models for behaviour genetics since selection has often been for few and well-defined behavioural traits. The aim of this study was to explore behavioural differences between selection lines in golden and Labrador retriever, in both of which a split between a common type (pet and conformation) and a field type (hunting) has occurred. We hypothesized that the behavioural profiles of the types would be similar in both breeds. Pedigree data and results from a standardized behavioural test from 902 goldens (698 common and 204 field) and 1672 Labradors (1023 and 649) were analysed. Principal component analysis revealed six behavioural components: curiosity, play interest, chase proneness, social curiosity, social greeting and threat display. Breed and type affected all components, but interestingly there was an interaction between breed and type for most components. For example, in Labradors the common type had higher curiosity than the field type (F_1,1668 = 18.359; P < 0.001), while the opposite was found in goldens (F_1,897 = 65.201; P < 0.001). Heritability estimates showed considerable genetic contributions to the behavioural variations in both breeds, but different heritabilities between the types within breeds was also found, suggesting different selection pressures. In conclusion, in spite of similar genetic origin and similar recent selection criteria, types behave differently in the breeds. This suggests that the genetic architecture related to behaviour differs between the breeds.

Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits

Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the F_ST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies.

Genome-wide association study identifies genomic regions of association for cruciate ligament rupture in Newfoundland dogs

Cranial cruciate ligament rupture (CCLR) is the most common cause of pelvic limb lameness in dogs. To investigate the genetic basis of canine CCLR, we conducted a genome-wide association study using a canine SNP array in Newfoundland pedigree dogs with and without CCLR (n = 96). We identified three main chromosomal regions of CCLR association (on chromosomes 1, 3 and 33). Each of these regions was confirmed by Sequenom genotyping in a further cohort of Newfoundlands (n = 271). The results, particularly SNPs identified in the SORCS2 and SEMA5B genes, suggest that there may be neurological pathways involved in susceptibility to canine CCLR.

That dog is smarter than you know: advances in understanding canine learning, memory, and cognition

Tests of canine cognition are now receiving much deserved attention. Not only are dogs excellent models for human anxiety-related conditions and those involving brain aging, but how dogs learn and problem solve are interesting stand-alone topics. A number of factors can affect learning at the molecular level including stress or distress, factors that affect olfaction, effects of breed and nutritional factors including that may affect available brain energy. This review provides an overview of how these factors may affect baseline learning and brain aging.