Removing exogenous information using pedigree data

Genomic rotational crossbreeding with advanced optimum contribution selection methods applied to simulated German Angler and German Holstein dairy cattle populations

Many local dairy cattle breeds are facing genetic extinction due to a large proportion of foreign genes, which have been introgressed in the past. In addition, the performance gap to popular high-yielding breeds is increasing, resulting in a risk of numeric extinction. In the present simulation study, a genomic rotational crossbreeding scheme with the high-yielding German Holstein breed and the numerically small German Angler breed was analysed with the aim to utilize heterosis effects in the crossbred animals. Simultaneously inbreeding was controlled, and the amount of Holstein introgression observed in the Angler breed was reduced. Different scenarios of implementing OCS methods for Angler individuals were evaluated, which differed in their restrictions regarding kinship, native kinship, as well as the amount of genetic contributions from German Holstein. The results showed that rotational crossbreeding can result in superior crossbred offspring compared to the purebred parental lines, whereby OCS methods can simultaneously restrict the increase in inbreeding and keep the Holstein contributions at their current level. However, reducing the amount of migrant contributions while restricting the increase in the native kinship in Angler turned out to be a costly restriction. The reason was that Angler with low genetic contributions from Holsteins tended to have similar Angler ancestors. Consequently, reducing Holstein contributions would considerably increase the native kinship in Angler if it were not constrained. The constraint on the native kinship made a constraint on the conventional kinship superfluous and caused it to increase at a much lower rate than envisaged. This led to both, a high genetic diversity and a low genetic gain. The high genetic diversity in Angler also resulted in lower and oscillating heterosis effects in the crossbred animals. Thus, the reduction of migrant contribution did not increase heterosis effects in the crossbred offspring, and did not result in superior crossbred offspring in general.

Associations between polymorphisms in the myostatin gene with calving difficulty and carcass merit in cattle

A fully functional myostatin gene inhibits muscle fiber growth. The objective of the present study was to quantify the association between 21 known myostatin mutations with both calving and carcass traits in 12 cattle breeds. The myostatin genotypes of 32,770 dam-progeny combinations were used in the association analysis of calving dystocia, with the genotypes of 129,803 animals used in the mixed model association analyses of carcass weight, conformation, and fat score. The mixed model included additive genetic, maternal, and permanent environmental effects where appropriate. The mutant genotypes of nt821, Q204X, and F94L were all associated (P < 0.01) with more calving difficulty when present in either the dam or the progeny. The nt821 deletion had the greatest association with calving difficulty when the homozygous deletion was present in either the calf (0.37 points greater calving difficulty score relative to calves carrying no copies of the deletion based on a one to four scale) or the dam (1.30 points greater calving difficulty score relative to dams carrying no copies of the deletion), although the association between the calf's nt821 genotype and calving difficulty differed depending on the nt821 genotype of the dam. With the exception of nt748_78, nt414, and nt374_51, all other seven segregating myostatin variants were associated (range of allele substitution effect size relative to animals with no copies of the mutant allele) with carcass weight (2.36 kg lighter to 15.56 kg heavier), all 10 segregating variants with conformation (0.15 units less conformed to 2.24 units more conformed assessed on a scale of 1 to 15), and all segregating variants other than E226X with carcass fat (0.23 units less carcass fat cover to 3.85 units more carcass fat cover assessed on a scale of 1 to 15). Of these, the F94L, Q204X, and nt821 mutations generally had the greatest association with all three carcass traits, giving rise to heavier and more conformed carcasses. Despite the antagonistic genetic relationship between calving difficulty and carcass traits, the nt374_51, F94L, and E226X mutations were all associated with improved carcass merit while having minimal expected consequences on calving difficulty. Thus, animals carrying these mutation(s) may have favorable genetic merit for calving difficulty and carcass merit. Furthermore, depending on the dam genotype, a bull with two copies of the nt821 mutation can produce progeny with improved carcass merit while minimizing calving problems.

Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe

Background

Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful.

Results

Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility.

Conclusions

This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible.

Key Genetic Parameters for Population Management

Population management has the primary task of maximizing the long-term competitiveness of a breed. Breeds compete with each other for being able to supply consumer demands at low costs and also for funds from conservation programs. The competition for consumer preference is won by breeds with high genetic gain for total merit who maintained a sufficiently high genetic diversity, whereas the competition for funds is won by breeds with high conservation value. The conservation value of a breed could be improved by increasing its contribution to the gene pool of the species. This may include the recovery of its original genetic background and the maintenance of a high genetic diversity at native haplotype segments. The primary objective of a breeding program depends on the genetic state of the population and its intended usage. In this paper, we review the key genetic parameters that are relevant for population management, compare the methods for estimating them, derive the formulas for predicting their value at a future time, and clarify their usage in various types of breeding programs that differ in their main objectives. These key parameters are kinships, native kinships, breeding values, Mendelian sampling variances, native contributions, and mutational effects. Population management currently experiences a transition from using pedigree-based estimates to marker-based estimates, which improves the accuracies of these estimates and thereby increases response to selection. In addition, improved measures of the factors that determine the competitiveness of a breed and utilize auxiliary parameters, such as Mendelian sampling variances, mutational effects, and native kinships, enable to improve further upon historic recommendations for genetic population management.

Managing genomes of conserved livestock breeds with historical introgression to decrease genetic overlap with other breeds

Recovering the native genetic background of a breed and increasing the founder genome equivalent (FGE) that is contributed by a breed to the gene pool of the species can increase its value for conservation. The suitability of several strategies was compared, whereby a hypothetical multi-breed population, the core set, was used to approximate the genetic diversity of the species. Twenty-five generations of management were simulated based on genotypes of German Angler cattle. The scenarios were compared when the kinship reached 0.10. The native contribution (NC) increased in a population with 400 births per generation from 0.317 to 0.706, whereas 1,000 births enabled to reach 0.894. This scenario maximized the NC, constrained the native kinship, and the kinship of the core set so that its genetic diversity could not decrease. It increased the proportions of mainstream breeds because their genes were removed from the target breed. A substantial increase of the FGE was achieved in some other scenarios, which arose from reduced genetic overlap and from increased diversity within the breed. The latter factor is especially important for breeds with high contributions to the core set.

Optimum contribution selection for animal breeding and conservation: the R package optiSel

Background

Selecting animals for breeding in the optimum way plays an essential role for the management of genetic resources and in selective breeding of livestock species. It requires to compute the optimum genetic contribution of each selection candidate to the next generation. Current software packages for optimum contribution selection (OCS) are not able to handle the main conflicting objectives of animal breeding programs simultaneously, which includes to increase genetic gain, to increase or to maintain genetic diversity, to recover the original genetic background of endangered breeds with historic introgression, and to maintain or increase genetic diversity at native alleles.

Results

The free R package optiSel offers functions for estimating the above mentioned parameters from pedigree and marker data, and for solving OCS problems. One parameter can be optimized, whereas the remaining ones can be constrained. The results reveal the optimum numbers of offspring of all selection candidates, and can subsequently be used for mate allocation. Different solvers can be used. Solver slsqp was superior when the genetic diversity at native alleles was to be maximized, whereas solvers cccp and cccp2 were superior for all other OCS problems.

Conclusion

Optimum contribution selection applied to local breeds requires special attention due to the conflicting objectives of their breeding programs. The free R package optiSel is an easy-to-use software taking these conflicting objectives into account.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2450-5) contains supplementary material, which is available to authorized users.

Long-Term Impact of Optimum Contribution Selection Strategies on Local Livestock Breeds with Historical Introgression Using the Example of German Angler Cattle

The long-term performance of different selection strategies was evaluated via simulation using the example of a local cattle breed, German Angler cattle. Different optimum contribution selection (OCS) approaches to maximize genetic gain were compared to a reference scenario without selection and truncation selection. The kinships and migrant contribution (MC) were estimated from genomic data. Truncation selection achieved the highest genetic gain but decreased diversity considerably at native alleles. It also caused the highest increase in MCs. Traditional OCS, which only constrains kinship, achieved almost the same genetic gain but also caused a small increase of MC and remarkably reduced the diversity of native alleles. When MC was required not to increase and the increase of kinship at native alleles was restricted, the MC levels and the diversity at native alleles were well managed, and the genetic gain was only slightly reduced. However, genetic progress was substantially lower in the scenario that aimed to recover the original genetic background. Truncation selection and traditional OCS selection both reduce the genetic originality of breeds with historical introgression. The inclusion of MC and kinship at native alleles as additional constraints in OCS showed great potential for conservation. Recovery of the original genetic background is possible but requires many generations of selection and reduces the genetic progress in performance traits. Hence, constraining MCs at their current values can be recommended to avoid further reduction of genetic originality.

Novel optimum contribution selection methods accounting for conflicting objectives in breeding programs for livestock breeds with historical migration

Background

Optimum contribution selection (OCS) is effective for increasing genetic gain, controlling the rate of inbreeding and enables maintenance of genetic diversity. However, this diversity may be caused by high migrant contributions (MC) in the population due to introgression of genetic material from other breeds, which can threaten the conservation of small local populations. Therefore, breeding objectives should not only focus on increasing genetic gains but also on maintaining genetic originality and diversity of native alleles. This study aimed at investigating whether OCS was improved by including MC and modified kinships that account for breed origin of alleles. Three objective functions were considered for minimizing kinship, minimizing MC and maximizing genetic gain in the offspring generation, and we investigated their effects on German Angler and Vorderwald cattle.

Results

In most scenarios, the results were similar for Angler and Vorderwald cattle. A significant positive correlation between MC and estimated breeding values of the selection candidates was observed for both breeds, thus traditional OCS would increase MC. Optimization was performed under the condition that the rate of inbreeding did not exceed 1% and at least 30% of the maximum progress was achieved for all other criteria. Although traditional OCS provided the highest breeding values under restriction of classical kinship, the magnitude of MC in the progeny generation was not controlled. When MC were constrained or minimized, the kinship at native alleles increased compared to the reference scenario. Thus, in addition to constraining MC, constraining kinship at native alleles is required to ensure that native genetic diversity is maintained. When kinship at native alleles was constrained, the classical kinship was automatically lowered in most cases and more sires were selected. However, the average breeding value in the next generation was also lower than that obtained with traditional OCS.

Conclusions

For local breeds with historical introgressions, current breeding programs should focus on increasing genetic gain and controlling inbreeding, as well as maintaining the genetic originality of the breeds and the diversity of native alleles via the inclusion of MC and kinship at native alleles in the OCS process.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0320-7) contains supplementary material, which is available to authorized users.

Genomics of a revived breed: Case study of the Belgian campine cattle

Through centuries of both natural and artificial selection, a variety of local cattle populations arose with highly specific phenotypes. However, the intensification and expansion of scale in animal production systems led to the predominance of a few highly productive cattle breeds. The loss of local populations is often considered irreversible and with them specific qualities and rare variants could be lost as well. Over these last years, the interest in these local breeds has increased again leading to increasing efforts to conserve these breeds or even revive lost populations, e.g. through the use of crosses with similar breeds. However, the remaining populations are expected to contain crossbred individuals resulting from introgressions. They are likely to carry exogenous genes that affect the breed's authenticity on a genomic level. Using the revived Campine breed as a case study, 289 individuals registered as purebreds were genotyped on the Illumina BovineSNP50. In addition, genomic information on the Illumina BovineHD and Illumina BovineSNP50 of ten breeds was available to assess the current population structure, genetic diversity, and introgression with phenotypically similar and/or historically related breeds. Introgression with Holstein and beef cattle genotypes was limited to only a few farms. While the current population shows a substantial amount of within-breed variation, the majority of genotypes can be separated from other breeds in the study, supporting the re-establishment of the Campine breed. The majority of the population is genetically close to the Deep Red (NL), Improved Red (NL) and Eastern Belgium Red and White (BE) cattle, breeds known for their historical ties to the Campine breed. This would support an open herdbook policy, thereby increasing the population size and consequently providing a more secure future for the breed.

Comparative genomics for biodiversity conservation

Genomic approaches are gathering momentum in biology and emerging opportunities lie in the creative use of comparative molecular methods for revealing the processes that influence diversity of wildlife. However, few comparative genomic studies are performed with explicit and specific objectives to aid conservation of wild populations. Here I provide a brief overview of comparative genomic approaches that offer specific benefits to biodiversity conservation. Because conservation examples are few, I draw on research from other areas to demonstrate how comparing genomic data across taxa may be used to inform the characterisation of conservation units and studies of hybridisation, as well as studies that provide conservation outcomes from a better understanding of the drivers of divergence. A comparative approach can also provide valuable insight into the threatening processes that impact rare species, such as emerging diseases and their management in conservation. In addition to these opportunities, I note areas where additional research is warranted. Overall, comparing and contrasting the genomic composition of threatened and other species provide several useful tools for helping to preserve the molecular biodiversity of the global ecosystem.

Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed

The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.

Short communication: Importance of introgression for milk traits in the German Vorderwald and Hinterwald cattle

The subject of the present study was to analyze the influence of genetic introgression on milk yield performance of the German local Vorderwald and Hinterwald cattle breeds. Deviations of milk yield, fat yield, and protein yield of cows as well as pedigree information were analyzed. A sire model was used to estimate genetic trend and effects of the migrant breeds. Migrant contributions to Vorderwald cattle were high and have been rising even in the recent past. The effects of these breeds on milk yield performance were positive. Montbéliarde cattle not only had the largest effect on milk production of Vorderwald cattle but also the highest genetic contribution to this breed. Genetic introgression with Montbéliarde continued until recently. This suggests that introgression of high-yielding breeds is still a preferred method for genetic improvement of local breeds, even though it diminishes their value for conservation. Hence, the current population management has too little focus on the preservation of genetic uniqueness. In comparison, migrant breed contributions to the Hinterwald cattle, a breed with a unique phenotype and an own niche, were moderate and almost constant over the time. For the Hinterwald cattle, no significant effect of migrant breeds could be detected, which suggests that population management has different priorities in different endangered breeds. We conclude that not only the registration of animals from local breeds but also the breeding programs themselves should be supported and need to be controlled.

The contribution of migrant breeds to the genetic gain of beef traits of German Vorderwald and Hinterwald cattle

During the past decades, migrant contributions have accumulated in many local breeds. Cross-breeding was carried out to mitigate the risk of inbreeding depression and to improve the performance of local breeds. However, breeding activities for local breeds were not as intensive and target oriented as for popular high-yielding breeds. Therefore, even if performance improved, the gap between the performance of local and popular breeds increased for many traits. Furthermore, the genetic originality of local breeds declined due to the increasing contributions of migrant breeds. This study examined the importance of migrant breed influences for the realization of breeding progress of beef traits of German Vorderwald and Hinterwald cattle. The results show that there is a high amount of migrant contributions and their effects on performance are substantial for most traits. The effect of the French cattle breed Montbéliard (p-value 0.014) on daily gain of Vorderwald bulls at test station was positive. The effects of Vorderwald ancestors (p-value for daily gain 0.007 and p-value for net gain 0.004) were positive for both traits under consideration in the population of Hinterwald cattle. Additionally, the effect of remaining breeds (p-value 0.030) on net gain of Hinterwald cattle in the field was also positive. The estimated effect of Fleckvieh ancestors on net gain of Hinterwald cattle was even larger but not significant. Breeding values adjusted for the effects of the migrant breeds showed little genetic trend.

Review: Genetics of helminth resistance in sheep

Karrow, N. A., Goliboski, K., Stonos, N., Schenkel, F. and Peregrine, A. 2014. Review: Genetics of helminth resistance in sheep. Can. J. Anim. Sci. 94: 1–9. Gastrointestinal helminth parasites are an important source of economic loss to sheep producers. A rapid increase in anthelmintic resistance has occurred around the globe; therefore, the industry is exploring alternative strategies such as genetic selection to control losses attributed to helminth infection. Since helminths have co-evolved with sheep for millions of years, natural selection for enhanced helminth resistance has occurred within certain breeds from various parts of the world. These breeds of sheep are being used to better understand the genetic aspects of helminth resistance. If the genetic variants that contribute to this phenotype can be identified, it may be possible to use selection strategies to introduce resistance alleles into other breeds or to increase their frequency within breeds. This review will provide an up-to-date overview of the pathology of helminth disease, the immune response to helminth infection, and the search for genes that confer helminth resistance.

Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds

Critically endangered breeds and populations are often crossed with more common breeds or subspecies. This results in genetic admixture that can be undesirable when it challenges the genetic integrity of wild and domestic populations, causing a loss in special characteristics or unique genetic material and ultimately extinction. Here, we present two genomic selection strategies, using genome-wide DNA markers, to recover the genomic content of the original endangered population from admixtures. Each strategy relies on the estimation of the proportion of nonintrogressed genome in individuals based on a different method: either genomic prediction or identification of breed-specific haplotypes. Then, breeding programs that remove introgressed genomic information can be designed. To test these strategies, we used empirical 50K SNP array data from two pure sheep breeds, Merino (used as target breed), Poll Dorset and an existing admixed population of both breeds. Sheep populations with varying degrees of introgression and admixture were simulated starting from these real genotypes. Both strategies were capable of identifying segment origin, and both removed up to the 100% of the Poll Dorset segments. While the selection process led to substantial inbreeding, we controlled it by imposing a minimum number of individuals contributing to the next generation.

Advantages of using molecular coancestry in the removal of introgressed genetic material

BACKGROUND

When introgression of undesired exogenous genetic material occurs in a population intended to remain pure, actions are necessary to recover the original background. It has been shown that genome-wide information can replace pedigree information for different objectives and is a valuable tool in the fields of genetic conservation and breeding. In this simulation study, molecular information provided by 50 000 SNP was used to minimise the molecular coancestry between individuals of an admixed population and the foreign individuals that originally introgressed a native population in order to remove the exogenous DNA.

RESULTS

This management method, which detects the 'purest' individuals to be used as parents for the next generation, allowed recovery of the native genetic background to a great extent in all simulated scenarios. However, it also caused an increase in inbreeding larger than expected because of the lower number of individuals selected as parents and the higher coancestry between them. In scenarios involving several introgression events the method was more efficient than in those involving a single introgression event because part of the genetic information was mixed with the native genetic material for a shorter period.

CONCLUSIONS

Genome-wide information can be used to identify the purest individuals via the minimisation of molecular coancestry between individuals of the admixed and exogenous populations. Removal of the undesired genetic material is more efficient with a molecular-based approach than with a pedigree-based approach.

Optimum contribution selection for conserved populations with historic migration

Background

In recent decades, local varieties of domesticated animal species have been frequently crossed with economically superior breeds which has resulted in considerable genetic contributions from migrants. Optimum contribution selection by maximizing gene diversity while constraining breeding values of the offspring or vice versa could eventually lead to the extinction of local breeds with historic migration because maximization of gene diversity or breeding values would be achieved by maximization of migrant contributions. Therefore, other objective functions are needed for these breeds.

Results

Different objective functions and side constraints were compared with respect to their ability to reduce migrant contributions, to increase the genome equivalents originating from native founders, and to conserve gene diversity. Additionally, a new method for monitoring the development of effective size for breeds with incomplete pedigree records was applied. Approaches were compared for Vorderwald cattle, Hinterwald cattle, and Limpurg cattle. Migrant contributions could be substantially decreased for these three breeds, but the potential to increase the native genome equivalents is limited.

Conclusions

The most promising approach was constraining migrant contributions while maximizing the conditional probability that two alleles randomly chosen from the offspring population are not identical by descent, given that both descend from native founders.

Molecular markers allow to remove introgressed genetic background: a simulation study

The maintenance of genetically differentiated populations can be important for several reasons (whether for wild species or domestic breeds of economic interest). When those populations are introgressed by foreign individuals, methods to eliminate the exogenous alleles can be implemented to recover the native genetic background. This study used computer simulations to explore the usefulness of several molecular based diagnostic approaches to recover of a native population after suffering an introgression event where some exogenous alleles were admixed for a few generations. To remove the exogenous alleles, different types of molecular markers were used in order to decide which of the available individuals contributed descendants to next generation and their number of offspring. Recovery was most efficient using diagnostic markers (i.e., with private alleles) and least efficient when using alleles present in both native and exogenous populations at different frequencies. The increased inbreeding was a side-effect of the management strategy. Both values (% of native alleles and inbreeding) were largely dependent on the amount of exogenous individuals entering the population and the number of generations of admixture that occurred prior to management.