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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. [ABSTRACT FROM AUTHOR]

Abstract 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.

Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect mi of the microbiota composition on the breeding value gi of an animal i is the conditional expectation of its breeding value, given the vector φi with microbiota frequencies, that is mi=Egi|φi. The breeding value gi of an animal can therefore be decomposed into a heritable contribution mi that arises from an altered microbiota composition and a heritable contribution pi that arises from altered metabolic pathways within the animal, so gi=mi+pi. Instead of selecting for breeding value g^i, an index comprising the two components m^i and p^i with appropriate weights, that is Ii=λ1m^i+λ2p^i, can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Genotype-by-environment interaction (GxE) has been widely reported in dairy cattle. One way to analyze GxE is to apply reaction norm models. The first derivative of a reaction norm is the environmental sensitivity (ES). In the present study we conducted a large-scale, genome-wide association analysis to identify single-nucleotide polymorphisms (SNPs) that affect general production (GP) and ES of milk traits in the German Holstein population. Sire estimates for GP and for ES were calculated from approximately 13 million daughter records by the use of linear reaction norm models. The daughters were offspring from 2297 sires. Sires were genotyped for 54k SNPs. The environment was defined as the average milk energy yield performance of the herds at the time during which the daughter observations were recorded. The sire estimates were used as observations in a genome-wide association analysis, using 1797 sires. Significant SNPs were confirmed in an independent validation set (500 sires of the same population). To separate GxE scaling and other GxE effects, the observations were log-transformed in some analyses. Results from the reaction norm model revealed GxE effects. Numerous significant SNPs were validated for both GP and ES. Many SNPs that affect GP also affect ES. We showed that ES of milk traits is a typical quantitative trait, genetically controlled by many genes with small effects and few genes with larger effect. A log-transformation of the observation resulted in a reduced number of validated SNPs for ES, pointing to genes that not only caused scaling GxE effects. The results will have implications for breeding for robustness in dairy cattle.