Dairy cattle breeding has historically focused on relatively small numbers of elite bulls as sires of sons. In recent years, even if generation intervals were reduced and more diverse sires of sons could have been selected, genomic selection has not fundamentally changed the fact that a large number of individuals are being analyzed. However, a relatively small number of elite bulls are still siring those animals. Therefore inbreeding-derived negative consequences in the gene pool have brought concern. The detrimental effects of non-additive genetic changes such as inbreeding depression and dominance have been widely disseminated while seriously affecting bioeconomically important parameters because of an antagonistic relationship between dairy production and reproductive traits. Therefore, the estimation of benefits and limitations of inbreeding and variance of the selection response deserves to be evaluated and discussed to preserve genetic variability, a significant concern in the selection of individuals for reproduction and production. Short-term strategies for genetic merit improvement through modern breeding programs have severely lowered high-producing dairy cattle fertility potential. Since the current selection programs potentially increase long-term costs, genetic diversity has decreased globally as a consequence. Therefore, a greater understanding of the potential that selection programs have for supporting long-term genetic sustainability and genetic diversity among dairy cattle populations should be prioritized in managing farm profitability. The present review provides a broad approach to current inbreeding-derived problems, identifying critical points to be solved and possible alternative strategies to control selection against homozygous haplotypes while maintaining sustained selection pressure. Moreover, this manuscript explores future perspectives, emphasizing theoretical applications and critical points, and strategies to avoid the adverse effects of inbreeding in dairy cattle. Finally, this review provides an overview of challenges that will soon require multidisciplinary approaches to managing dairy cattle populations, intending to combine increases in productive trait phenotypes with improvements in reproductive, health, welfare, linear conformation, and adaptability traits into the foreseeable future.

Genetic improvement, without control of inbreeding, can go to loss of genetic variability, reducing the potential for genetic gains in the domestic populations. The aim of this study was to analyze the population structure and the inbreeding depression in Campolina horses. Phenotype information from 43 465 individuals was analyzed, data provided by the Campolina Breeders Association. A pedigree file containing 107 951 horses was used to connected the phenotyped individuals. The inbreeding coefficient was performed by use of the diagonal of the relationship matrix and the genealogical parameters were computed using proper softwares. The effective population size was estimated based on the rate of inbreeding and census information, and the stratification of the population was verified by the average relationship coefficient between animals born in different regions of Brazil. The effects of inbreeding on morphological traits were made by the use of inbreeding coefficient as a covariate in the model of random regression. The inbreeding coefficient increased from 1990 on, impacting effective population size and, consequently, shrinking genetic variability. The paternal inbreeding was greater than maternal, which may be attributed to the preference for inbred animals in reproduction. The average genetic relationship coefficient of animals born in different states was lower than individuals born within the same state. The increase in the inbreeding coefficient was negatively associated with all studied traits, showing the importance to avoid genetic losses in the long term. Although results do not indicate a severe narrowing of the population until the present date, the average relationship coefficient shows signs of increase, which could cause a drastic reduction in genetic variability if inbred mating is not successfully controlled in the Campolina horse population.

Inbreeding has been associated with the impairment of reproductive performance in many cattle breeds. Although the usage of reproductive biotechnologies has been increasing in bovine populations, not much attention has been given to the impact of inbreeding over cow’s performance on artificial reproduction. The objective of this study was to estimate the impact of inbreeding on in vitro embryo production in a Guzerá breed population. The inbreeding coefficient (F), calculated as half of the co-ancestry of the individual’s parents, was used as an estimate of inbreeding. The inbreeding coefficients of the donor, sire (used on in vitro fertilization) and of the embryos were included, separately, in the proposed models either as classificatory or continuous variables (linear and quadratic effects). The percentage of non-inbred individuals (or embryos) and mean F of donors, embryos and sires were 29.38%; 35.76%; 42.86% and 1.98±2.68; 1.32±3.13; 2.08±2.79, respectively. Two different models were considered, one for oocyte production traits and other for embryo production traits. The increase of F of the donor significantly (P<0.05) impaired the number of viable oocytes (NOV), number of grade I oocytes (NGI) and number of cleaved embryos (NCLV). Moreover, the donor’s F influenced the percentage of grade I oocytes (PGI), percentage of viable embryos (PEMB) and percentage of cleaved embryos that turned into embryos (PCXE). No significant (P>0.05) effects were observed for the sire (father of the embryos) inbreeding coefficient over the traits analysed. Embryo’s F influenced (P<0.05) the number of viable embryos (NEMB), percentage of viable embryos (PEMB) and percentage of cleaved embryos that turn into embryos (PCXE). Results suggested that an increase in the inbreeding coefficient might impair the embryos ability to survive through challenges imposed by the in vitro environment. Submitting highly inbred Guzerá female donors to in vitro embryo production may, in the long-term, have negative implications on the number of embryos obtained per cow and increase the relative costs of the improvement programmes based on this technology. High levels of inbreeding should be avoided when selecting Guzerá female donors and planning in vitro fertilization mating.

A cleistogamous species consists of individuals that produce both chasmogamous (open, CH) and cleistogamous (permanently closed, CL) flowers, which facilitates a mixed-mating system. In contrast to what one might expect, CL (obligately selfed) seeds and the plants derived from them can be more fit than CH (potentially outcrossed) seeds and the plants they give rise to. Our aim was to review some theoretical aspects of mixed mating in relation to retention of both CH and CL in cleistogamous species and to determine if data on germination support the notion that CL is advantageous over that of CH. Based on germination (or seedling emergence) of CH vs CL seeds in 29 species in 21 genera and 11 families of monocots and eudicots, CL seeds germinated better in 107 and equally well as in 64 of 252 case studies as CH seeds (67.9%), and the (CH < CL):(CH > CL) ratio was 107/81 (1.32). We conclude that our study lends support to the notion that production of CL seeds by cleistogamous species is advantageous over that of CH seeds. Retention of CH by CL species may be due to the need to prevent complete selfing (s= 1.0) and thus total inbreeding depression (δ), which theory predicts would decrease reproductive success. Some caveats concerning the results of comparative studies on the germination biology of CH vs CL seeds of amphicarpic sensu stricto Fabaceae species and Commelina benghalensis and the aerial cleistogamous grass Danthonia spicata are discussed.

Weeds represent a major cause of agricultural losses worldwide. Most weeds share a common set of life history characteristics that predispose them to weediness, two of which are self-compatibility, which allows for ease of colonization through reproductive assurance, and high trait plasticity, which allows for tolerance of a wide variety of environments and abiotic conditions. However, self-fertilization typically comes at the cost of inbreeding depression. This study investigates the role of inbreeding depression and trait plasticity under abiotic stress in the tall morningglory, a widespread self-compatible agricultural weed in the southeastern United States. Results show very little inbreeding depression in this species, likely due to purging of deleterious alleles through repeated founder events in agricultural landscapes. In contrast, abiotic stress induced substantial plasticity in ecophysiological traits, reproductive traits, and biomass allocation. In terms of performance, drought sharply impacted reproduction but not vegetative growth, and nitrogen limitation sharply impacted both. These findings are applicable to the control of weedy morningglory and underscore the usefulness of evolutionary ecology to weed management.

Self-fertilization (or selfing), defined as the fusion of male and female reproductive cells originating from the same individual, is the most extreme case of inbreeding. Although most hermaphroditic organisms are in principle able to self-fertilize, this reproductive strategy is commonly associated with a major disadvantage: inbreeding depression. Deleterious effects due to the loss of genetic diversity have been documented in numerous organisms including parasites. Here we studied the effects of inbreeding depression on the offspring of the progenetic trematode Coitocaecum parvum. The parasite can use 2 alternative life-history strategies: either it matures early, via progenesis, and produces eggs by selfing in its second intermediate host, or it waits and reproduces by out-crossing in its definitive host. We measured various key parameters of parasite fitness (i.e. hatching and multiplication rates, infectivity, survival) in offspring produced by both selfing and out-crossing. Altogether, we found no significant difference in the fitness of offspring from progenetic (selfing) and adult (out-crossing) parents. In addition, we found no evidence that either strategy (progenesis or the normal three-host cycle) is heritable, i.e. the strategy adopted by offspring is independent of that used by their parents. Although it is unclear why both reproductive strategies are maintained in C. parvum populations, our conclusion is that producing eggs by selfing has few, if any, negative effects on parasite offspring. Inbreeding depression is unlikely to be a factor acting on the maintenance of the normal three-host life cycle, and thus out-crossing, in C. parvum populations.

Inbreeding depression is well documented in insects but the degree to which inbreeding depression varies among populations within species, and among traits within populations, is poorly studied in insects other than Drosophila. Inbreeding depression was examined in two long-term laboratory colonies of the seed beetle, Callosobruchus maculatus (Fabricius), which are used frequently as models for experiments in ecology, evolution and behaviour. Inbreeding depression in these laboratory colonies are compared with one recently field-collected population of a different seed beetle, Stator limbatus Horn. Inbreeding reduced embryogenesis, egg hatch and larval survival in both species, such that eggs produced by sib matings were >17% less likely to produce an adult offspring. Inbred larvae also took 4–6% longer to develop to emergence in both species. Inbreeding depression varied among the measured traits but did not differ between the two populations of C. maculatus for any trait, despite the large geographic distance between source populations (western Africa vs. southern India). Inbreeding depression was similar in magnitude between C. maculatus and S. limbatus. This study demonstrates that these laboratory populations of C. maculatus harbour substantial genetic loads, similar to the genetic load of populations of S. limbatus recently collected from the field.

Many hermaphroditic parasites reproduce by both cross-fertilization and self-fertilization. To understand the maintenance of such mixed mating systems it is necessary to compare the fitness consequences of the two reproductive modes. This has, however, almost never been done in the context of host–parasite coevolution. Here we show the consequences of outcrossing and selfing in an advanced life-stage of the cestode Schistocephalus solidus, i.e. in its second intermediate host, the three-spined stickleback (Gasterosteus aculeatus). Each juvenile stickleback was simultaneously exposed to 2 experimentally infected copepods, one harbouring outcrossed the other selfed parasites. At 60 days p.i. parasites were removed from the fish's body cavity and, with microsatellite markers, assigned to either outcrossed or selfed origin. Prevalence was not significantly higher in outcrossed parasites. However, those fish that were infected contained significantly more outcrossed than selfed parasites. Thus the probability of a selfed parasite to progress in the life-cycle is reduced in the second intermediate host. Furthermore, we found that even the multiply infected fish increased in weight during the experiment. Nevertheless, total worm weight in multiply infected fish was significantly lower than in singly infected ones, which thus might be a parasite life-history strategy.

The aims of this study were to examine population structure and inbreeding trend in six dog breeds in Finland and to assess the inbreeding depression for hip and elbow dysplasia. Data consisted of 289 569 dogs, of which 36 924 dogs also had a record for hip and/or elbow dysplasia screening. From the early 1980s onwards, inbreeding trends were decreasing in the Golden Retriever, the Labrador Retriever, the Rough Collie and the Rottweiler, probably as a result of importations of dogs, and somewhat increasing in the Finnish Hound and the German Shepherd. When analysed per generation, observed mean inbreeding coefficients were higher than the expected ones in each breed, indicating that breeders have not actively avoided inbreeding. As a class effect, the inbreeding level was significant only for hip dysplasia in the Labrador Retriever and the German Shepherd breeds. As a regression, inbreeding level of a dog had only a minor effect on both of the dysplasias. Hip dysplasia in the Labrador Retriever appeared to be more influenced by longer term aggregation of homozygosity (long-term inbreeding) in animals than by shorter-term inbreeding. When analysed from two data sets with a minimum of five and two ancestral generations for each dog in the data, a statistically significant association between hip dysplasia and inbreeding for the Labrador Retriever could be detected only in the former data set.

A genetic algorithm (GA) was used to find optimal male and female age distributions in a natural mating system that maximizes cumulative response to mass selection over a 20-year time horizon for the case where inbreeding affects reproduction at 0·0 (F-0) and 0·1 (F-10) per 0·1 inbreeding coefficient. Twenty breeding female population sizes were considered ranging from 25 to 500 breeding females distributed across five age groups. Loss of response due to inbreeding effects on reproduction ranged from 19.4% and 15.5% in small breeding female populations to 2.5% and 5.2% in large breeding female populations when number of males was fixed (FX) or optimized (OP), respectively. OP resulted in an increase in response over FX ranging from 0·0 % to 69.3% for F-0 and 0·0 % to 77.6% for F-10. The potential loss of genetic gain that resulted from ignoring the inbreeding effects upon reproduction when they really existed ranged from 0·1 % to 44.6%. The potential loss of genetic gain that resulted from including inbreeding effects upon reproduction when they did not exist ranged from 0·1% to 3.9%. Optimal male and female age structures depended upon breeding female population size, the number of breeding males and inbreeding effects. Ignoring inbreeding effects upon reproduction may result in over estimation of response to selection. Use of a GA allowed accounting for complex relationships in the optimization.

This paper continues a series of studies of the allogamous raphid diatom Achnanthes longipes, which has a complex reproductive system combining unisexual, bisexual and monoecious behaviour. Following earlier work on the effects of inbreeding in the progeny of crosses between two unisexual clones, we studied the progeny of clones that are capable of a high degree of selfing in monoclonal culture (‘monoecious clones’). Three generations of selfed progeny were examined. In addition, we investigated the F1 generation obtained after crossing two different monoecious clones. Monoecious clones produced monoecious or, more rarely, bisexual progeny, but did not give rise to unisexual progeny. As in inbred lineages made by crossing closely related unisexual clones, inbreeding in monoecious lineages leads to a reduction in the number of gametes formed by the gametangia, from two to one. Inbred clones exhibit marked inbreeding depression and only three inbred generations were possible in monoecious lineages. In the third, final inbred generation, monoecious sexual reproduction was initiated in monoclonal cultures but gametes rarely fused and none of the auxospores and initial cells that were formed were viable; this also occurred when the inbred clones were crossed with any of the other clones available. The significance of inbreeding and other aspects of the breeding system in A. longipes is discussed.

An experimental herd of Large White pigs was established in 1931 and maintained as a closed population until 1992. The complete -pedigree (410 boars and 916 sows) has been analysed to measure along the succesive cohorts of breeding animals: thefounder representation and allele survival, the evolution ofcoancestry and inbreeding and the components of inbreeding due to each founder. Inferences about genetic and phenotypic parameters and effects of dam and litter inbreeding on litter size were obtained, using Bayesian techniques, from 2612 litter records. A significant mean reduction of 0·27 piglets born and 0·39 live born for each 10% of litter inbreeding was found but also evidence of variation among founder lineages in inbreeding depression. Alleles contributing to inbreeding depression were descendent from specific founder lineages.