Effect of non-random mating on genomic and BLUP selection schemes

Background

The risk of long-term unequal contribution of mating pairs to the gene pool is that deleterious recessive genes can be expressed. Such consequences could be alleviated by appropriately designing and optimizing breeding schemes i.e. by improving selection and mating procedures.

Methods

We studied the effect of mating designs, random, minimum coancestry and minimum covariance of ancestral contributions on rate of inbreeding and genetic gain for schemes with different information sources, i.e. sib test or own performance records, different genetic evaluation methods, i.e. BLUP or genomic selection, and different family structures, i.e. factorial or pair-wise.

Results

Results showed that substantial differences in rates of inbreeding due to mating design were present under schemes with a pair-wise family structure, for which minimum coancestry turned out to be more effective to generate lower rates of inbreeding. Specifically, substantial reductions in rates of inbreeding were observed in schemes using sib test records and BLUP evaluation. However, with a factorial family structure, differences in rates of inbreeding due mating designs were minor. Moreover, non-random mating had only a small effect in breeding schemes that used genomic evaluation, regardless of the information source.

Conclusions

It was concluded that minimum coancestry remains an efficient mating design when BLUP is used for genetic evaluation or when the size of the population is small, whereas the effect of non-random mating is smaller in schemes using genomic evaluation.     

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.     

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.     

Maintaining genetic diversity using molecular coancestry: the effect of marker density and effective population size

Background

The most efficient method to maintain genetic diversity in populations under conservation programmes is to optimize, for each potential parent, the number of offspring left to the next generation by minimizing the global coancestry. Coancestry is usually calculated from genealogical data but molecular markers can be used to replace genealogical coancestry with molecular coancestry. Recent studies showed that optimizing contributions based on coancestry calculated from a large number of SNP markers can maintain higher levels of diversity than optimizing contributions based on genealogical data. In this study, we investigated how SNP density and effective population size impact the use of molecular coancestry to maintain diversity.

Results

At low SNP densities, the genetic diversity maintained using genealogical coancestry for optimization was higher than that maintained using molecular coancestry. The performance of molecular coancestry improved with increasing marker density, and, for the scenarios evaluated, it was as efficient as genealogical coancestry if SNP density reached at least 3 times the effective population size.However, increasing SNP density resulted in reduced returns in terms of maintained diversity. While a benefit of 12% was achieved when marker density increased from 10 to 100 SNP/Morgan, the benefit was only 2% when it increased from 100 to 500 SNP/Morgan.

Conclusions

The marker density of most SNP chips already available for farm animals is sufficient for molecular coancestry to outperform genealogical coancestry in conservation programmes aimed at maintaining genetic diversity. For the purpose of effectively maintaining genetic diversity, a marker density of around 500 SNPs/Morgan can be considered as the most cost effective density when developing SNP chips for new species. Since the costs to develop SNP chips are decreasing, chips with 500 SNPs/Morgan should become available in a short-term horizon for non domestic species.     

Genome-Wide Estimates of Coancestry,Inbreeding and Effective Population Size in the Spanish Holstein Population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.     

Genetic structure,relationships and admixture with wild relatives in native pig breeds from Iberia and its islands

Background

Native pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies.

Methods

A panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results.

Results

Genetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and within-breed components of genetic diversity.

Conclusions

Native pig breeds in Iberia reveal high levels of genetic diversity, a solid breed structure and a clear organization in well-defined clusters.     

A note on the rationale for estimating genealogical coancestry from molecular markers

Background

Genetic relatedness or similarity between individuals is a key concept in population, quantitative and conservation genetics. When the pedigree of a population is available and assuming a founder population from which the genealogical records start, genetic relatedness between individuals can be estimated by the coancestry coefficient. If pedigree data is lacking or incomplete, estimation of the genetic similarity between individuals relies on molecular markers, using either molecular coancestry or molecular covariance. Some relationships between genealogical and molecular coancestries and covariances have already been described in the literature.

Methods

We show how the expected values of the empirical measures of similarity based on molecular marker data are functions of the genealogical coancestry. From these formulas, it is easy to derive estimators of genealogical coancestry from molecular data. We include variation of allelic frequencies in the estimators.

Results

The estimators are illustrated with simulated examples and with a real dataset from dairy cattle. In general, estimators are accurate and only slightly biased. From the real data set, estimators based on covariances are more compatible with genealogical coancestries than those based on molecular coancestries. A frequently used estimator based on the average of estimated coancestries produced inflated coancestries and numerical instability. The consequences of unknown gene frequencies in the founder population are briefly discussed, along with alternatives to overcome this limitation.

Conclusions

Estimators of genealogical coancestry based on molecular data are easy to derive. Estimators based on molecular covariance are more accurate than those based on identity by state. A correction considering the random distribution of allelic frequencies improves accuracy of these estimators, especially for populations with very strong drift.     

Accuracy of estimated breeding values with genomic information on males,females, or both: an example on broiler chicken

Background

As more and more genotypes become available, accuracy of genomic evaluations can potentially increase. However, the impact of genotype data on accuracy depends on the structure of the genotyped cohort. For populations such as dairy cattle, the greatest benefit has come from genotyping sires with high accuracy, whereas the benefit due to adding genotypes from cows was smaller. In broiler chicken breeding programs, males have less progeny than dairy bulls, females have more progeny than dairy cows, and most production traits are recorded for both sexes. Consequently, genotyping both sexes in broiler chickens may be more advantageous than in dairy cattle.

Methods

We studied the contribution of genotypes from males and females using a real dataset with genotypes on 15 723 broiler chickens. Genomic evaluations used three training sets that included only males (4648), only females (8100), and both sexes (12 748). Realized accuracies of genomic estimated breeding values (GEBV) were used to evaluate the benefit of including genotypes for different training populations on genomic predictions of young genotyped chickens.

Results

Using genotypes on males, the average increase in accuracy of GEBV over pedigree-based EBV for males and females was 12 and 1 percentage points, respectively. Using female genotypes, this increase was 1 and 18 percentage points, respectively. Using genotypes of both sexes increased accuracies by 19 points for males and 20 points for females. For two traits with similar heritabilities and amounts of information, realized accuracies from cross-validation were lower for the trait that was under strong selection.

Conclusions

Overall, genotyping males and females improves predictions of all young genotyped chickens, regardless of sex. Therefore, when males and females both contribute to genetic progress of the population, genotyping both sexes may be the best option.     

Inclusion of cow records in genomic evaluations and impact on bias due to preferential treatment

Background

Today, genomic evaluations are an essential feature of dairy cattle breeding. Initially, genomic evaluation targeted young bulls but recently, a rapidly increasing number of females (both heifers and cows) are being genotyped. A rising issue is whether and how own performance of genotyped cows should be included in genomic evaluations. The purpose of this study was to assess the impact of including yield deviations, i.e. own performance of cows, in genomic evaluations.

Methods

Two different genomic evaluations were performed: one including only reliable daughter yield deviations of proven bulls based on their non-genotyped daughters, and one including both daughter yield deviations for males and own yield deviations for genotyped females. Milk yield, the trait most prone to preferential treatment, and somatic cell count, for which such a bias is very unlikely, were studied. Data consisted of two groups of animals from the three main dairy breeds in France: 11 884 elite females genotyped by breeding companies and 7032 cows genotyped for a research project (and considered as randomly selected from the commercial population).

Results

For several measures that could be related to preferential treatment bias, the elite group presented a different pattern of estimated breeding values for milk yield compared to the other combinations of trait and group: for instance, for milk yield, the average difference between estimated breeding values with or without own yield deviations was significantly different from 0 for this group. Correlations between estimated breeding values with or without yield deviations were lower for elite females than for randomly selected cows for milk yield but were very similar for somatic cell count.

Conclusions

This study demonstrated that including own milk performance of elite females leads to biased (over-estimated) genomic evaluations. Thus, milk production records of elite cows require specific treatment in genomic evaluation.     

Sexual dimorphism in a dioecious population of the wind-pollinated herb Mercurialis annua: the interactive effects of resource availability and competition

Background and Aims

Male-biased sex allocation commonly occurs in wind-pollinated hermaphroditic plants, and is often positively associated with size, notably in terms of height. Currently, it is not well established whether a corresponding pattern holds for dioecious plants: do males of wind-pollinated species exhibit greater reproductive allocation than females? Here, sexual dimorphism is investigated in terms of life history trade-offs in a dioecious population of the wind-pollinated ruderal herb Mercurialis annua.

Methods

The allocation strategies of males and females grown under different soil nutrient availability and competitive (i.e. no, male or female competitor) regimes were compared.

Key Results

Male reproductive allocation increased disproportionately with biomass, and was greater than that of females when grown in rich soils. Sexual morphs differentially adjusted their reproductive allocation in response to local environmental conditions. In particular, males reduced their reproductive allocation in poor soils, whereas females increased theirs, especially when competing with another female rather than growing alone. Finally, males displayed smaller above-ground vegetative sizes than females, but neither nutrient availability nor competition had a strong independent effect on relative size disparities between the sexes.

Conclusions

Selection appears to favour plasticity in reproductive allocation in dioecious M. annua, thereby maintaining a relatively constant size hierarchy between sexual morphs. In common with other dioecious species, there seems to be little divergence in the niches occupied by males and females of M. annua.     

Changing domesticity of Aedes aegypti in northern peninsular Malaysia: reproductive consequences and potential epidemiological implications

Background

The domestic dengue vector Aedes aegypti mosquitoes breed in indoor containers. However, in northern peninsular Malaysia, they show equal preference for breeding in both indoor and outdoor habitats. To evaluate the epidemiological implications of this peridomestic adaptation, we examined whether Ae. aegypti exhibits decreased survival, gonotrophic activity, and fecundity due to lack of host availability and the changing breeding behavior.

Methodology/Principal Findings

This yearlong field surveillance identified Ae. aegypti breeding in outdoor containers on an enormous scale. Through a sequence of experiments incorporating outdoors and indoors adapting as well as adapted populations, we observed that indoors provided better environment for the survival of Ae. aegypti and the observed death patterns could be explained on the basis of a difference in body size. The duration of gonotrophic period was much shorter in large-bodied females. Fecundity tended to be greater in indoor acclimated females. We also found increased tendency to multiple feeding in outdoors adapted females, which were smaller in size compared to their outdoors breeding counterparts.

Conclusion/Significance

The data presented here suggest that acclimatization of Ae. aegypti to the outdoor environment may not decrease its lifespan or gonotrophic activity but rather increase breeding opportunities (increased number of discarded containers outdoors), the rate of larval development, but small body sizes at emergence. Size is likely to be correlated with disease transmission. In general, small size in Aedes females will favor increased blood-feeding frequency resulting in higher population sizes and disease occurrence.     

Economic aspects of implementing genomic evaluations in a pig sire line breeding scheme

Background

Replacing pedigree-based BLUP evaluations by genomic evaluations in pig breeding schemes can result in greater selection accuracy and genetic gains, especially for traits with limited phenotypes. However, this methodological change would generate additional costs. The objective of this study was to determine whether additional expenditures would be more profitably devoted to implementing genomic evaluations or to increasing phenotyping capacity while retaining traditional evaluations.

Methods

Stochastic simulation was used to simulate a population with 1050 breeding females and 50 boars that was selected for 10 years for a breeding goal with two uncorrelated traits with heritabilities of 0.4. The reference breeding scheme was based on phenotyping 13 770 candidates per year for trait 1 and 270 sibs of candidates per year for trait 2, with selection based on pedigree-based BLUP estimated breeding values. Increased expenditures were allocated to either increasing the phenotyping capacity for trait 2 while maintaining traditional evaluations, or to implementing genomic selection. The genomic scheme was based on two training populations: one for trait 2, consisting of phenotyped sibs of the candidates whose number increased from 1000 to 3430 over time, and one for trait 1, consisting of the selection candidates. Several genomic scenarios were tested, where the size of the training population for trait 1, and the number of genotyped candidates pre-selected based on their parental estimated breeding value, varied.

Results

Both approaches resulted in higher genetic trends for the population breeding goal and lower rates of inbreeding compared to the reference scheme. However, even a very marked increase in phenotyping capacity for trait 2 could not match improvements achieved with genomic selection when the number of genotyped candidates was large. Genotyping just a limited number of pre-selected candidates significantly reduced the extra costs, while preserving most of the benefits in terms of genetic trends and inbreeding. Implementing genomic evaluations was the most efficient approach when major expenditure was possible, whereas increasing phenotypes was preferable when limited resources were available.

Conclusions

Economic decisions on implementing genomic evaluations in a pig nucleus population must take account of population characteristics, phenotyping and genotyping costs, and available funds.     

A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes

Background

Knowing the phase of marker genotype data can be useful in genome-wide association studies, because it makes it possible to use analysis frameworks that account for identity by descent or parent of origin of alleles and it can lead to a large increase in data quantities via genotype or sequence imputation. Long-range phasing and haplotype library imputation constitute a fast and accurate method to impute phase for SNP data.

Methods

A long-range phasing and haplotype library imputation algorithm was developed. It combines information from surrogate parents and long haplotypes to resolve phase in a manner that is not dependent on the family structure of a dataset or on the presence of pedigree information.

Results

The algorithm performed well in both simulated and real livestock and human datasets in terms of both phasing accuracy and computation efficiency. The percentage of alleles that could be phased in both simulated and real datasets of varying size generally exceeded 98% while the percentage of alleles incorrectly phased in simulated data was generally less than 0.5%. The accuracy of phasing was affected by dataset size, with lower accuracy for dataset sizes less than 1000, but was not affected by effective population size, family data structure, presence or absence of pedigree information, and SNP density. The method was computationally fast. In comparison to a commonly used statistical method (fastPHASE), the current method made about 8% less phasing mistakes and ran about 26 times faster for a small dataset. For larger datasets, the differences in computational time are expected to be even greater. A computer program implementing these methods has been made available.

Conclusions

The algorithm and software developed in this study make feasible the routine phasing of high-density SNP chips in large datasets.     

Increased genetic gains in sheep,beef and dairy breeding programs from using female reproductive technologies combined with optimal contribution selection and genomic breeding values

Background

Female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile in vitro embryo production and embryo transfer (JIVET) can boost rates of genetic gain but they can also increase rates of inbreeding. Inbreeding can be managed using the principles of optimal contribution selection (OCS), which maximizes genetic gain while placing a penalty on the rate of inbreeding. We evaluated the potential benefits and synergies that exist between genomic selection (GS) and reproductive technologies under OCS for sheep and cattle breeding programs.

Methods

Various breeding program scenarios were simulated stochastically including: (1) a sheep breeding program for the selection of a single trait that could be measured either early or late in life; (2) a beef breeding program with an early or late trait; and (3) a dairy breeding program with a sex limited trait. OCS was applied using a range of penalties (severe to no penalty) on co-ancestry of selection candidates, with the possibility of using multiple ovulation and embryo transfer (MOET) and/or juvenile in vitro embryo production and embryo transfer (JIVET) for females. Each breeding program was simulated with and without genomic selection.

Results

All breeding programs could be penalized to result in an inbreeding rate of 1 % increase per generation. The addition of MOET to artificial insemination or natural breeding (AI/N), without the use of GS yielded an extra 25 to 60 % genetic gain. The further addition of JIVET did not yield an extra genetic gain. When GS was used, MOET and MOET + JIVET programs increased rates of genetic gain by 38 to 76 % and 51 to 81 % compared to AI/N, respectively.

Conclusions

Large increases in genetic gain were found across species when female reproductive technologies combined with genomic selection were applied and inbreeding was managed, especially for breeding programs that focus on the selection of traits measured late in life or that are sex-limited. Optimal contribution selection was an effective tool to optimally allocate different combinations of reproductive technologies. Applying a range of penalties to co-ancestry of selection candidates allows a comprehensive exploration of the inbreeding vs. genetic gain space.     

The effect of genomic information on optimal contribution selection in livestock breeding programs

Background

Long-term benefits in animal breeding programs require that increases in genetic merit be balanced with the need to maintain diversity (lost due to inbreeding). This can be achieved by using optimal contribution selection. The availability of high-density DNA marker information enables the incorporation of genomic data into optimal contribution selection but this raises the question about how this information affects the balance between genetic merit and diversity.

Methods

The effect of using genomic information in optimal contribution selection was examined based on simulated and real data on dairy bulls. We compared the genetic merit of selected animals at various levels of co-ancestry restrictions when using estimated breeding values based on parent average, genomic or progeny test information. Furthermore, we estimated the proportion of variation in estimated breeding values that is due to within-family differences.

Results

Optimal selection on genomic estimated breeding values increased genetic gain. Genetic merit was further increased using genomic rather than pedigree-based measures of co-ancestry under an inbreeding restriction policy. Using genomic instead of pedigree relationships to restrict inbreeding had a significant effect only when the population consisted of many large full-sib families; with a half-sib family structure, no difference was observed. In real data from dairy bulls, optimal contribution selection based on genomic estimated breeding values allowed for additional improvements in genetic merit at low to moderate inbreeding levels. Genomic estimated breeding values were more accurate and showed more within-family variation than parent average breeding values; for genomic estimated breeding values, 30 to 40% of the variation was due to within-family differences. Finally, there was no difference between constraining inbreeding via pedigree or genomic relationships in the real data.

Conclusions

The use of genomic estimated breeding values increased genetic gain in optimal contribution selection. Genomic estimated breeding values were more accurate and showed more within-family variation, which led to higher genetic gains for the same restriction on inbreeding. Using genomic relationships to restrict inbreeding provided no additional gain, except in the case of very large full-sib families.     

Indoor-Breeding of Aedes albopictus in Northern Peninsular Malaysia and Its Potential Epidemiological Implications

Background

The mosquito Ae. albopictus is usually adapted to the peri-domestic environment and typically breeds outdoors. However, we observed its larvae in most containers within homes in northern peninsular Malaysia. To anticipate the epidemiological implications of this indoor-breeding, we assessed some fitness traits affecting vectorial capacity during colonization process. Specifically, we examined whether Ae. albopictus exhibits increased survival, gonotrophic activity and fecundity due to the potential increase in blood feeding opportunities.

Methodology/Principal Findings

In a series of experiments involving outdoors and indoors breeding populations, we found that Ae. albopictus lives longer in the indoor environment. We also observed increased nighttime biting activity and lifetime fecundity in indoor/domestic adapted females, although they were similar to recently colonized females in body size.

Conclusion/Significance

Taken together these data suggest that accommodation of Ae. albopictus to indoor/domestic environment may increase its lifespan, blood feeding success, nuisance and thus vectorial capacity (both in terms of increased vector-host contacts and vector population density). These changes in the breeding behavior of Ae. albopictus, a potential vector of several human pathogens including dengue viruses, require special attention.     

Genomic selection requires genomic control of inbreeding

Background

In the past, pedigree relationships were used to control and monitor inbreeding because genomic relationships among selection candidates were not available until recently. The aim of this study was to understand the consequences for genetic variability across the genome when genomic information is used to estimate breeding values and in managing the inbreeding generated in the course of selection on genome-enhanced estimated breeding values.

Methods

These consequences were measured by genetic gain, pedigree- and genome-based rates of inbreeding, and local inbreeding across the genome. Breeding schemes were compared by simulating truncation selection or optimum contribution selection with a restriction on pedigree- or genome-based inbreeding, and with selection using estimated breeding values based on genome- or pedigree-based BLUP. Trait information was recorded on full-sibs of the candidates.

Results

When the information used to estimate breeding values and to constrain rates of inbreeding were either both pedigree-based or both genome-based, rates of genomic inbreeding were close to the desired values and the identical-by-descent profiles were reasonably uniform across the genome. However, with a pedigree-based inbreeding constraint and genome-based estimated breeding values, genomic rates of inbreeding were much higher than expected. With pedigree-instead of genome-based estimated breeding values, the impact of the largest QTL on the breeding values was much smaller, resulting in a more uniform genome-wide identical-by-descent profile but genomic rates of inbreeding were still higher than expected based on pedigree relationships, because they measure the inbreeding at a neutral locus not linked to any QTL. Neutral loci did not exist here, where there were 100 QTL on each chromosome. With a pedigree-based inbreeding constraint and genome-based estimated breeding values, genomic rates of inbreeding substantially exceeded the value of its constraint. In contrast, with a genome-based inbreeding constraint and genome-based estimated breeding values, marker frequencies changed, but this change was limited by the inbreeding constraint at the marker position.

Conclusions

To control inbreeding, it is necessary to account for it on the same basis as what is used to estimate breeding values, i.e. pedigree-based inbreeding control with traditional pedigree-based BLUP estimated breeding values and genome-based inbreeding control with genome-based estimated breeding values.     

Comparison of molecular breeding values based on within- and across-breed training in beef cattle

Background

Although the efficacy of genomic predictors based on within-breed training looks promising, it is necessary to develop and evaluate across-breed predictors for the technology to be fully applied in the beef industry. The efficacies of genomic predictors trained in one breed and utilized to predict genetic merit in differing breeds based on simulation studies have been reported, as have the efficacies of predictors trained using data from multiple breeds to predict the genetic merit of purebreds. However, comparable studies using beef cattle field data have not been reported.

Methods

Molecular breeding values for weaning and yearling weight were derived and evaluated using a database containing BovineSNP50 genotypes for 7294 animals from 13 breeds in the training set and 2277 animals from seven breeds (Angus, Red Angus, Hereford, Charolais, Gelbvieh, Limousin, and Simmental) in the evaluation set. Six single-breed and four across-breed genomic predictors were trained using pooled data from purebred animals. Molecular breeding values were evaluated using field data, including genotypes for 2227 animals and phenotypic records of animals born in 2008 or later. Accuracies of molecular breeding values were estimated based on the genetic correlation between the molecular breeding value and trait phenotype.

Results

With one exception, the estimated genetic correlations of within-breed molecular breeding values with trait phenotype were greater than 0.28 when evaluated in the breed used for training. Most estimated genetic correlations for the across-breed trained molecular breeding values were moderate (> 0.30). When molecular breeding values were evaluated in breeds that were not in the training set, estimated genetic correlations clustered around zero.

Conclusions

Even for closely related breeds, within- or across-breed trained molecular breeding values have limited prediction accuracy for breeds that were not in the training set. For breeds in the training set, across- and within-breed trained molecular breeding values had similar accuracies. The benefit of adding data from other breeds to a within-breed training population is the ability to produce molecular breeding values that are more robust across breeds and these can be utilized until enough training data has been accumulated to allow for a within-breed training set.     

Long-term response to genomic selection: effects of estimation method and reference population structure for different genetic architectures

Background

Genomic selection has become an important tool in the genetic improvement of animals and plants. The objective of this study was to investigate the impacts of breeding value estimation method, reference population structure, and trait genetic architecture, on long-term response to genomic selection without updating marker effects.

Methods

Three methods were used to estimate genomic breeding values: a BLUP method with relationships estimated from genome-wide markers (GBLUP), a Bayesian method, and a partial least squares regression method (PLSR). A shallow (individuals from one generation) or deep reference population (individuals from five generations) was used with each method. The effects of the different selection approaches were compared under four different genetic architectures for the trait under selection. Selection was based on one of the three genomic breeding values, on pedigree BLUP breeding values, or performed at random. Selection continued for ten generations.

Results

Differences in long-term selection response were small. For a genetic architecture with a very small number of three to four quantitative trait loci (QTL), the Bayesian method achieved a response that was 0.05 to 0.1 genetic standard deviation higher than other methods in generation 10. For genetic architectures with approximately 30 to 300 QTL, PLSR (shallow reference) or GBLUP (deep reference) had an average advantage of 0.2 genetic standard deviation over the Bayesian method in generation 10. GBLUP resulted in 0.6% and 0.9% less inbreeding than PLSR and BM and on average a one third smaller reduction of genetic variance. Responses in early generations were greater with the shallow reference population while long-term response was not affected by reference population structure.

Conclusions

The ranking of estimation methods was different with than without selection. Under selection, applying GBLUP led to lower inbreeding and a smaller reduction of genetic variance while a similar response to selection was achieved. The reference population structure had a limited effect on long-term accuracy and response. Use of a shallow reference population, most closely related to the selection candidates, gave early benefits while in later generations, when marker effects were not updated, the estimation of marker effects based on a deeper reference population did not pay off.     

Functional characterization of gynodioecy in Fragaria vesca ssp. bracteata (Rosaceae)

Background and Aims

Gynodioecy is a phylogenetically widespread and important sexual system where females coexist with hermaphrodites. Because dioecy can arise from gynodioecy, characterization of gynodioecy in close relatives of dioecious and sub-dioecious species can provide insight into this transition. Thus, we sought to determine whether Fragaria vesca ssp. bracteata, a close relative to F. chiloensis and F. virginiana, exhibits the functional and population genetic hallmarks of a gynodioecious species.

Methods

We compared reproductive allocation of females and hermaphrodites grown in the greenhouse and estimated genetic diversity (allelic diversity, heterozygosity) and inbreeding coefficients for field-collected adults of both sexes using simple sequence repeat (SSR) markers. We estimated mating system and early seed fitness from open-pollinated families of both sex morphs.

Key Results

Under greenhouse conditions, females and hermaphrodites allocated similarly to all reproductive traits except flower number, and, as a consequence, females produced 30 % fewer seeds per plant than hermaphrodites. Under natural conditions, hermaphrodites produce seeds by self-fertilization approx. 75 % of the time, and females produced outcrossed seeds with very little biparental inbreeding. Consistent with inbreeding depression, seeds from open-pollinated hermaphrodites were less likely to germinate than those from females, and family-level estimates of hermaphrodite selfing rates were negatively correlated with germination success and speed. Furthermore, estimates of inbreeding depression based on genetic markers and population genetic theory indicate that inbreeding depression in the field could be high.

Conclusions

The joint consideration of allocation and mating system suggests that compensation may be sufficient to maintain females given the current understanding of sex determination. Fragaria vesca ssp. bracteata exhibited similar sex morph-dependent patterns of mating system and genetic diversity, but less reproductive trait dimorphism, than its sub-dioecious and dioecious congeners.