Increased Levels Of Inbreeding Research Articles

Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares.

The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the “inbreeding depression” effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level (ρ = −0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (−0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (FROH) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.

17 Increased inbreeding levels negatively affect sperm kinetics and motility in Purebred Spanish horses

Reproductive performance is one of the key factors in livestock production. It is well known that reproductive traits are influenced by several genetic factors, such as the increase of individual inbreeding levels, which are associated with changes in sperm motility and shape in several species. In horses, the increase in inbreeding is a common problem because of the reduction in effective population size and the increase in selection intensity observed in several breeds. However, studies assessing the effect of high levels of inbreeding on the sperm quality of stallions are scarce. In the present study, we aimed to determine the effect of increased inbreeding levels and age on the sperm motility patterns of Purebred Spanish horses (PRE). We performed kinetic characterisation of 557 sperm samples of 82 PRE stallions aged between 3 and16 years, using computer-assisted sperm analysis (Androvision™, Minitube). We evaluated 5 parameters in 6 different fields per sample: curved line velocity (VCL, µm/s), velocity average path (VAP, µm/s), velocity straight line (VSL, µm/s), amplitude of lateral head displacement (ALH, µm), and beat-cross frequency (BCF, Hz). We determined the pedigree-based inbreeding coefficient (Fped) based on ∼300,000 PRE pedigree records to evaluate the inbreeding effect. Individuals were separated into 2 groups: highly inbred (n=339) and lowly inbred (n=218) according to an F value of 12.5%. Differences between groups were analysed using a generalized linear model. The analysis did not show significant differences (P>0.05) in the variables analysed with respect to the age of stallions. However, VAP, VCL, and AHL were lower in highly inbred than in lowly inbred animals (P<0.05), suggesting less velocity and amplitude of head displacement. In the case of BCF, no significant differences (P>0.05) were observed between the two study groups. In conclusion, age did not affect sperm quality parameters in the age group of stallions analysed. In addition, we demonstrated that high inbreeding coefficient reduced the mean velocity and trajectory pattern of spermatozoa in PRE.

Consanguineous marriages among Andalusian Gitanos/Calé: a genealogical analysis (1925-2006).

Using data from the family and genealogical reconstitutions of the Gitano population of 22 contiguous localities in eastern Andalusia, Spain, this study analysed the intensity, structure and historical evolution of consanguinity in 3056 couples formed from 1925 to 2006. Of these unions, 54.8% were consanguineous, and 28.7% involved relatives up to and including second cousins, resulting in a mean coefficient of inbreeding up to the third degree α3 = 12.4 × 10-3. The rest of the consanguineous unions (26.1% of all) involved more-distant relatives, such as third cousins, fourth cousins and so forth. When all consanguinity degrees found in the genealogical reconstitution were considered, the total mean coefficient of inbreeding was αt = 14.8 × 10-3. The merging of families and pedigrees generated a complex genealogical network with many inbreeding loops and important founder effects. This network revealed a high rate (62%) of Multiple Consanguineous Marriages (MCMs) in which second and subsequent consanguineous ties increased inbreeding levels by a fifth (20.5%). The accumulation of multiple degrees of distant relatedness, many of which had little social or biological importance, has contributed to a significant increase in inbreeding rates. Among Gitano people, intra-family marriages have remained common in the last decades, in sharp contrast to other Spanish populations. Hence the highest rates of close consanguinity (34%) and inbreeding (α3 = 14.6 × 10-3) were found in the 1960s, the decade that saw the onset of Spain's socioeconomic modernization, internationalization and massive migration. These are among the highest rates of inbreeding found in any European population, including the most endogamous Spanish isolates. They reveal marriage strategies not constrained primarily by geographical barriers, but by ethnocultural separation. Interestingly, in recent decades mixed marriages have been increasing rapidly in this minority, although they are compatible with high rates of consanguinity. Gitano secular endogamy is breaking up, but not uniformly.

Genetic effects of rainforest fragmentation in an early successional tree (Elaeocarpus grandis).

Rainforests in Australia and around the world have been extensively cleared and degraded. It is essential to recognize the changes in population diversity and dynamics that follow habitat fragmentation if better conservation and management strategies are to be developed. This study is an investigation of the medium term (over 100 years) effects of rainforest fragmentation on a long-lived, early successional tree species within a habitat matrix that includes various types of fragmented and undisturbed sites. Five microsatellite loci were used to assess the level and distribution of genetic variation across the southern range of Elaeocarpus grandis (Elaeocarpaceae). In all, 21 sites were sampled to provide a direct comparison between fragmented and undisturbed populations. Overall levels of diversity (A=3.4, He=0.568, f=0.094) were higher than those of closely related endemic species, but lower than those recorded across other rainforest trees. No significant genetic structure was detected across this species, suggesting the existence of efficient dispersal and colonization mechanisms responsible for the maintenance of gene flow. Rainforest fragments, and in particular those within the extensively cleared Big Scrub, show a trend for increased inbreeding levels caused by a loss of heterozygosity within juvenile cohorts. However, the overall rate of genetic decline within fragmented rainforests appears to be more subtle in E. grandis than across other species. A combination of ecological attributes and evolutionary history is likely to have contributed to this outcome and need to be considered in future rainforest restoration projects.

Embryonic genetic load for a neotropical conifer, Pinus patula Schiede et Deppe

Genetic loads tend to be higher for widely distributed boreal and temperate pines compared to other plants and most animals. Although genetic loads have not been estimated for neotropical pines, it seems likely that genetic loads will be lower due to disjunct population structure and high rates of endemism. Embryonic genetic load is reported for a founder population of Pinus patula, a neotropical species used as a Zimbabwe exotic. The study was based on a novel orthogonal inbred mating design with 5 grandparents and 12 parents equally represented at four levels of inbreeding. Contrary to predictions, P. patula had an average of six to eight embryonic lethal equivalents, a genetic load comparable to temperate and boreal pines. Embryo viability declined linearly with increased inbreeding levels (F=0-0.5), supporting the independent lethal model. P. patula appears to have a stable embryo-lethal system despite small population sizes.

Prediction of additive and dominance effects in selected or unselected populations with inbreeding

A genetic model with either 64 or 1,600 unlinked biallelic loci and complete dominance was used to study prediction of additive and dominance effects in selected or unselected populations with inbreeding. For each locus the initial frequency of the favourable allele was 0.2, 0.5, or 0.8 in different alternatives, while the initial narrow-sense heritability was fixed at 0.30. A population of size 40 (20 males and 20 females) was simulated 1,000 times for five generations. In each generation 5 males and 10 or 20 females were mated, with each mating producing four or two offspring, respectively. Breeding individuals were selected randomly, on own phenotypic performance or such yielding increased inbreeding levels in subsequent generations. A statistical model containing individual additive and dominance effects but ignoring changes in mean and genetic covariances associated with dominance due to inbreeding resulted in significantly biased predictions of both effects in generations with inbreeding. Bias, assessed as the average difference between predicted and simulated genetic effects in each generation, increased almost linearly with the inbreeding coefficient. In a second statistical model the average effect of inbreeding on the mean was accounted for by a regression of phenotypic value on the inbreeding coefficient. The total dominance effect of an individual in that case was the sum of the average effect of inbreeding and an individual effect of dominance. Despite a high mean inbreeding coefficient (up to 0.35), predictions of additive and dominance effects obtained with this model were empirically unbiased for each initial frequency in the absence of selection and 64 unlinked loci. With phenotypic selection of 5 males and only 10 females in each generation and 64 loci, however, predictions of additive and dominance effects were significantly biased. Observed biases disappeared with 1,600 loci for allelic frequencies at 0.2 and 0.5. Bias was due to a considerable change in allelic frequency with phenotypic selection. Ignoring both the covariance between additive and dominance effects with inbreeding and the change in dominance variance due to inbreeding did not significantly bias prediction of additive and dominance effects in selected or unselected populations with inbreeding.

Effects of mating system in Japanese quail

A 17-generation selection experiment was conducted to study direct and correlated responses to mass selection under a mating system with alternating generations of full-sib inbreeding and wide outbreeding (population I) as compared with a mass selected, randomly mated population (population II). The selection criterion was an index of total egg mass to 78 days divided by adult female body weight. Estimates of heritabilities and genetic correlations are reported. Estimated heritabilities for the index were 0.38±0.04 and 0.29±0.05 in population I and II, respectively. Realized heritabilites were 0.10±0.05 and 0.12±0.03. For most traits studied the mean phenotypic values in the cyclic mated population decreased for inbred generations. Increased inbreeding levels also caused outbred generation means of population I to decrease through the first six or seven generations. After this period of adaptation to inbreeding selection response was positive for the index and positively correlated traits. Total response to selection under the cyclic inbred-outbred mating system did not exceed selection response made under random mating. However, the rate of response in the cyclically mated population exceeded that in the randomly mated population in later generations when the cyclically mated population had apparently adapted to inbreeding.