Genetic diversity and historic introgression in German Angler and Red Dual Purpose cattle and possibilities to reverse introgression

Recovering native uniqueness has major importance for breeds with historic introgression. The aim of the study was to estimate population genetic parameters for two local red cattle breeds from Northern Germany and to study possibilities to reverse introgression. Genealogical information consisted of 90,783 individuals for German Angler and 187,255 individuals for Red Dual-Purpose cattle breed, with additional information on sex, born, breed, status, and conventional breeding values. It is concluded that the native genetic contribution could be included as an additional trait in the total merit index in order to recover a part of the native genetic background. Native contributions should be estimated in the long term from marker data in order to account for Mendelian sampling. The maintenance of a sufficient genetic diversity of native alleles can be achieved by an advanced OCS with appropriate constraints.     

Genetic correlations between production with disease resistance and fertility in dairy cattle and consequences for total merit selection

Twelve years of data from progeny‐test results of 1486 Swedish Red and White (SRB) and 756 Swedish Black and White (SLB) AI bulls were analysed to provide estimates of genetic correlations between yield of protein and three health‐ and fertility traits. For both breeds, the correlations were unfavourable (r_G= —0.13 to —0.37). The effects of negative genetic correlations (compared to a situation with genetic correlations with zero values) on the b‐values in the total merit index of bulls were rather small but the effects on the estimated genetic gain were large. The effect of not including health and fertility traits in the index, although included in the breeding goal, resulted in a 9–10% reduced accuracy of estimated breeding values for total merit and thus a corresponding loss in total gain.     

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.     

Genetic differences among native and modern cattle breeds in Lithuania based on milk protein loci polymorphism

The intrabreed and interbreed genetic diversity of Lithuanian cattle breeds - two native, namely Lithuanian Light Grey and Lithuanian White-Backed and two modern, namely Lithuanian Red and Lithuanian Black and White was investigated by determination of genetic markers: 4 milk protein systems, Alpha(s1)-casein, Kappa-casein, Beta-casein and Beta-lactoglobulin, which are comprised of 12 different milk protein types. According to results, the B type of Alpha(s1)-casein was found as predominant in all four studied breeds. The most common A and B types of Kappa-casein were found at high frequency in all investigated cattle breeds. All investigated Lithuanian dairy cattle breeds had high frequency of Beta-lactoglobulin whey protein B types, with the highest frequency in Lithuanian Red breed, and the lowest in Lithuanian Light Grey. After investigation the diversity of alleles and genotypes of milk proteins in Lithuanian dairy cattle breeds was determined that, Lithuanian Red breed was distinguished private C allele and BC genotype of Beta-lactoglobulin and CC genotype of Alpha(s1)-casein. The interbreed genetic diversity was estimated by a principal component analysis (PCA). The first principal component (PC) explains 63.39% and the second principal component (PC) explains 33.67% of the genetics diversity between the breeds. Principal component analysis, suggests the hypothesis that native Lithuanian White Backed and Lithuanian Light Grey breeds still have traits tracing to old native populations.     

Genetic and phenotypic parameters for conformation and yield traits in three Swiss dairy cattle breeds

This study presents genetic parameters for conformation traits and their genetic and phenotypic correlations with milk production traits and somatic cell score (SCS) in three Swiss dairy cattle breeds. Data on first lactations from Holstein (67 839), Brown Swiss (173 372) and Red & White breeds (53 784) were available. Analysed conformation traits were stature and heart girth (both in cm), and linear scores of body depth, rump width, dairy character or muscularity, and body condition score (only in Holstein). A sire model, with relationships among sires, was used for all breeds and traits and variance components were estimated using AS‐REML. Heritabilities for stature were high (0.6–0.8), and for the linear type traits ranged from 0.3 to 0.5, for all breeds. Genetic correlations with production traits (milk, fat and protein yield) and SCS differed between the dairy breeds. Most markedly, stronger correlations were found between SCS and some conformation traits in Brown Swiss and Red & White, indicating that a focus on a larger and more ‘dairy’ type in these breeds would lead to increased SCS. Another marked difference was that rump width correlated positively with milk yield traits in Holstein and Red & White, but negative in Brown Swiss. Results indicate that conformation traits generally can be used as predictors for various purposes in dairy cattle breeding, but may require specific adaptation for each breed.     

Application of aggregate genotype in beef cattle breeding

Abstract

When developing total merit indices (TMI's), estimated breeding values (EBV's) may be lacking for several traits. Methodology exists to address these challenges, calculating index weights using economic values and genetic (co)variances between traits included in the TMI and aggregate genotype. TMI's including production and functional traits were developed for beef breeds in the Norwegian breeding scheme, and potential for genetic gain was evaluated. Selection based on the TMI developed in this study was found to improve growth and carcass quality, while genetic deterioration was expected for calving difficulty. Alternative selection indices were applied to avoid these effects, but reduced the genetic gain for production traits. The results of our study show that is possible to achieve genetic gain in most economically important traits for beef cattle by using a TMI. When additional EBV's and genetic correlations become available, these should be included into the TMI for further improvement.     

Correlations Analysis between Polymorphism of 3’-UTR in MSTN Gene and Slaughter Traits of China Red Steppe

In order to study the effect of myostatin (MSTN) gene on the meat performance of Local Yellow cattle in China,selecting 2 Local cattle breeds (Grassland Red bull,Yanbian cattle) as the research object,four binary hybrid cattle group (Germany Yellow cattle×Simmental,Limousin×Simmental,Charolais×Simmental and Red Angus×Simmental) as reference.PCR-RFLP and DNA sequencing methods were conducted to detect single nucleotide polymorphism of MSTN gene in two Chinese native cattle and four cross cattle,and analyzed the correlations between single nucleotide polymorphism of China Red Steppe MSTN gene and slaughter traits.The sequence analysis showed that there was no mutations in the MSTN gene exon 3,a C5358A mutation of 3'-UTR of MSTN gene was found,which made the AclⅠrestriction enzyme site disappeared,all cattle groups showed polymorphism which was formed two genes as A,C, and 3 genotypes as AA,CA and CC, respectively.The research results suggested that AA genotype in groups of four hybrid cattle had dominant advantage and the genotype frequency was apparently higher than two groups of Chinese Native cattle for the test of independence,allele A was expressed the preferential allelic,the frequencies of CA,CC and AA genotypes showed a little variation between two cross cattle and Native cattle,and the frequency of allele C was apparently higher than allele A,so allele C was designed the preferential allelic in the local population.While correlations between different genotypes of China Red Steppe and slaughter traits analysis showed that AA genotype individual net meat percentage and eye muscle area were significantly higher than CA and CC genotype individuals (P<0.05),but other slaughter straits had no significant differences in three genotypes(P>0.05).These results provided a useful reference for research of the meat performance of China Red Steppe in the molecular breeding field.     

肉牛杂交亲本遗传距离与杂种优势的相关性研究

利用11个微卫星标记研究川南山地黄牛、海福特牛、黑安格斯牛、红安格斯牛、利木赞牛、西门塔尔牛、德国黄牛的遗传多样性,分析肉牛亲本间微卫星标记遗传距离与体尺、体重杂种优势间的相关性。结果表明:11个微卫星基因座平均有效等位基因数为4.5422,7个牛种的多态信息含量在0.3434~0.4207,平均杂合度为0.6868~0.8413,7个牛种均具有丰富的多态性。亲本间遗传距离与体尺、体重杂种优势间相关系数偏小(-0.003~0.304),均未达到显著水平,用微卫星标记遗传距离预测肉牛体尺、体重杂种优势还有待进一步探讨。     

The role of agro-ecological factors and transboundary transhumance in shaping the genetic diversity in four indigenous cattle populations of Benin

The indigenous cattle population of Benin is a diverse mix of taurine and hybrid breeds shaped by diverse ecological and climatic conditions with eight agro-ecological zones (AEZ). Presumably, the taurine breeds face current endangerment due to ongoing indicine introgression following climate change and transboundary transhumance. The aim of the study was to investigate the genetic diversity and population structure of the indigenous breeds Lagune, Somba, Pabli and Borgou considering spatial agro-ecological and socio-economic factors (transhumance) based on 50k SNP and microsatellite data. Among the four sampled breeds, six genetic clusters were identified using model-free (discriminant analysis of principal components) and model-based (TESS and ADMIXTURE) methods separating taurine from hybrid breeds. Results based on an extension with publicly available historic SNP data sets from taurine and indicine West African cattle and additional outgroups provided additional insight into changes of genetic structure in the sampled breeds over time. Both taurine breeds, Somba and Lagune, showed a stable foundation but also spatially limited partial indicine introgression associated with transhumance leading to high genetic diversity. In addition, we found evidence for spatial diversity and changes in genetic structure over time in the Borgou breed in comparison of our samples with the historic samples which could be explained by potential continuous indicine introgression into the Borgou breed in two sample regions. Results for the Pabli breed do not conclusively point to full absorbance by the Borgou in comparison with all available Borgou samples. Further research is needed in this regard.     

隆林牛与郏县红牛线粒体DNA全基因组遗传多样性比较研究

摘　要：［目的］本研究旨在从基因组水平探究隆林牛和郏县红牛的线粒体DNA（mtDNA）全基因组遗传多样性与母系起源,并对2个黄牛品种的mtDNA全基因组遗传多样性进行比较分析。［方法］采用全基因组重测序及生物信息学方法。［结果］在15头隆林牛和28头郏县红牛mtDNA全基因组序列中,共检测到36种单倍型,其中郏县红牛有26种单倍型,隆林牛仅有8种单倍型,2个黄牛品种共享2种单倍型。郏县红牛和隆林牛的平均单倍型多样度（Hd）分别为1.000和0.943,平均核苷酸多样度（Pi）分别为0.0080和0.0053,表明其遗传多样性丰富。构建的系统发育树表明,隆林牛和郏县红牛具有瘤牛和普通牛两个母系支系。［结论］隆林牛以瘤牛起源为主,郏县红牛为普通牛与瘤牛的混合起源,这2个地方黄牛品种具有独特的母系遗传信息,表现出明显的母系遗传差异。     

Identification of differential selection traces in two Polish cattle breeds

Genetic improvement of animals based on artificial selection is leading to changes in the frequency of genes related to desirable production traits. The changes are reflected by the neutral, intergenic single nucleotide polymorphims (SNPs) being in long‐range linkage disequilibrium with functional polymorphisms. Genome‐wide SNP analysis tools designed for cattle, allow for scanning divergences in allelic frequencies between distinct breeds and thus for identification of genomic regions which were divergently selected in breeds' histories. In this study, by using Bovine SNP50 assay, we attempted to identify genomic regions showing the highest differences in allele frequencies between two distinct cattle breeds – preserved, unselected Polish Red breed and highly selected Holstein cattle. Our study revealed 19 genomic regions encompassing 55 protein‐coding genes and numerous quantitative trait loci which potentially may underlie some of the phenotypic traits distinguishing the breeds.     

Genetic components in contemporary Faroe Islands Cattle as revealed by microsatellite analysis

The gene pool of indigenous Faroe Islands Cattle is strongly affected by crossing with Norwegian Red. In this study, the genetic structure in 191 animals representing five North European cattle breeds (Faroe Islands, Icelandic, Blacksided Troender, Western Fjord and Norwegian Red) and the genetic admixture in the contemporary Faroe Islands Cattle at the population and individual level were evaluated using 20 polymorphic microsatellite loci. Only 6.7% of the total genetic variation could be attributed to the differences amongst the breeds. The factorial correspondence analysis based on all allele frequencies could hardly reveal a divergence between Faroe Islands Cattle and Norwegian Red. In addition, a Neighbor‐Net tree constructed to examine the allocation of individuals of Faroe Islands Cattle and Norwegian Red provided a detailed interrelationship network for all the 72 animals. An estimation of the population admixture proportion showed a strong genetic contribution by Norwegian Red (47.3%) in the contemporary Faroe Islands Cattle. On the other hand, individual admixture analysis demonstrated that only seven of the individual Faroe Islands Cattle analysed, which also showed more traditional colour patterns, could be assigned to the Faroe Islands Cattle cluster, probably representing the breed's remaining purebred animals. Strategies for preserving the original native genes in Faroe Islands Cattle should be considered in order to prevent the breed from becoming extinct and to strengthen the breed's capability in future breeding programmes.     

The Agersoe cattle: the last remnants of the Danish island cattle (Bos taurus)?

A phenotypically interesting strain of cattle existed on the small island of Agersoe, on the west coast of Zealand, Denmark, in the beginning of the last decade. The cattle share a great resemblance to the extinct Danish breed, the Island cattle. The objective of this study was to genetically characterize the Agersoe cattle, using microsatellites, amplified fragment length polymorphism (AFLP) and mtDNA markers, and analyse the genetic variability within the breed and the genetic relationship to 14 European breeds with focus on the Red Danish and Jutland breed. The results show diversity in nuclear markers comparable to that of modern breeds and that the Agersoe cattle are separable from the two native breeds. The absence of inbreeding and the degree of genetic diversity are taken as a sign of recent admixture. The Agersoe cattle did not exhibit a consistent association with any of the European breeds. Several arguments based on this survey have been put forward in favour of characterizing the Agersoe cattle as being the last remnants of the Danish Island Cattle.     

Effects of breed proportion and components of heterosis for semen traits in a composite cattle breed

The aim of this study was to estimate the non‐additive genetic effects of the dominance component of heterosis as well as epistatic loss on semen traits in admixed Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Heterosis is the additional gain in productivity or fitness of cross‐bred progeny over the mid‐purebred parental populations. Intralocus gene interaction usually has a positive effect, while epistatic loss generally reduces productivity or fitness due to lack of evolutionarily established interactions of genes from different breeds. Genotypic data on 38,205 SNP of 818 admixed, as well as 148 RHF and 213 SI bulls as the parental breeds were used to predict breed origin of alleles. The genomewide locus‐specific breed ancestries of individuals were used to calculate effects of breed difference as well as the dominance component of heterosis, while proxies for two definitions of epistatic loss were derived from 100,000 random pairs of loci. The average Holstein Friesian ancestry in admixed bulls was estimated 0.82. Results of fitting different linear mixed models showed including the dominance component of heterosis considerably improved the model adequacy for three of the four traits. Inclusion of epistatic loss increased the accuracy of the models only for our new definition of the epistatic effect for two traits, while the other definition was so highly correlated with the dominance component that statistical separation was impossible.     

The impact of using old germplasm on genetic merit and diversity—A cattle breed case study

Artificial selection and high genetic gains in livestock breeds led to a loss of genetic diversity. Current genetic diversity conservation actions focus on long‐term maintenance of breeds under selection. Gene banks play a role in such actions by storing genetic materials for future use and the recent development of genomic information is facilitating characterization of gene bank material for better use. Using the Meuse‐Rhine‐Issel Dutch cattle breed as a case study, we inferred the potential role of germplasm of old individuals for genetic diversity conservation of the current population. First, we described the evolution of genetic merit and diversity over time and then we applied the optimal contribution (OC) strategy to select individuals for maximizing genetic diversity, or maximizing genetic merit while constraining loss of genetic diversity. In the past decades, genetic merit increased while genetic diversity decreased. Genetic merit and diversity were both higher in an OC scenario restricting the rate of inbreeding when old individuals were considered for selection, compared to considering only animals from the current population. Thus, our study shows that gene bank material, in the form of old individuals, has the potential to support long‐term maintenance and selection of breeds.     

Development of sustainable performance index based on production,reproduction, health and longevity for genetic improvement of Sahiwal cattle

An attempt was made for the first time in India to develop the performance indices for quantifying the relative emphasis to be given to production, reproduction, health and longevity traits for selection and genetic improvement of Sahiwal cattle in a sustainable manner. The study was conducted using information related to various production, reproduction, health and longevity traits spread over a period of 29 years in Sahiwal cattle. Using income and expenditure method, the relative economic values for 305 days milk yield (305DMY), average daily milk yield (ADMY), calving to first insemination interval (CFI), days open (DO) and longevity (LNG) were estimated as 1, 1, −6.62, −6.62 and 5.96 in Sahiwal cattle. A total of three performance indices were constructed using three-trait combination, that is production, reproduction and longevity before and after excluding the days suffered by the animals. Correlation between the aggregate genotype and index (R_IH) was computed to determine the accuracy of each performance index, and based on highest R_IH value, best performance index was identified for selection of Sahiwal cattle. Developed indices were further assessed for robustness by increasing the relative economic values of the traits by 25% and 50%. The performance index (305DMY, DO and LNG) was found to be the best index before as well as after excluding days suffered by the animals, but in later case emphasis to be given to different traits was found to be more balanced. The best index indicated that about 47, 42 and 11% relative emphasis to be assigned to 305 days milk yield, days open and longevity for selection of Sahiwal animals for sustainable genetic improvement.     

Technical note: Constrained optimization of breed composition in composite populations to balance net merit and risk

We developed a method to derive optimum composite genotypes when the proportion of a specific breed (or combination of breeds) in the composite is constrained to a desired level. The method allows development of composites that balance net merit according to available parameters and reflects the production system and(or) risk preference, particularly when traits in the breeding objective do not represent all traits important for production. The method can also be used to evaluate the cost of constraining breed use. For example, when the true optimal composite is difficult to obtain in the time frame available to the producer, the predicted merit of the composite with breed proportion restricted to those that are obtainable in practice can be compared with the predicted merit of the true optimum composite. In a case study the method is used to optimize a tropical composite using Brahman, Charolais, and Belmont Red breeds. The proportion of Charolais is to be constrained to 50%. Using growth parameters from a tropical crossbreeding experiment, the unconstrained optimum composite was 32.5% Brahman, 11.1% Belmont Red, and 56.3% Charolais. When the proportion of Charolais in the composite was constrained to 50%, optimum proportions of Brahman and Belmont Red were 33.9% and 16.1% respectively. In the case study net merit (annualized profit per cow exposed, $), as defined by the growth parameters, was .2% less than that of the unconstrained optimum composite.     

Theoretical efficiency of multiple-trait quantitative trait loci-assisted selection

The effectiveness of five selection methods for genetic improvement of net merit comprising trait 1 of low heritability (h² = 0.1) and trait 2 of high heritability (h² = 0.4) was examined: (i) two‐trait quantitative trait loci (QTL)‐assisted selection; (ii) partial QTL‐assisted selection based on trait 1; (iii) partial QTL‐assisted selection based on trait 2; (iv) QTL‐only selection; and (v) conventional selection index without QTL information. These selection methods were compared under 72 scenarios with different combinations of the relative economic weights, the genetic correlations between traits, the ratio of QTL variance to total genetic variance of the trait, and the ratio of genetic variances between traits. The results suggest that the detection of QTL for multiple‐trait QTL‐assisted selection is more important when the index traits are negatively correlated than when they are positively correlated. In contrast to literature reports that single‐trait marker‐assisted selection (MAS) is the most efficient for low heritability traits, this study found that the identified QTL of the low heritability trait contributed negligibly to total response in net merit. This is because multiple‐trait QTL‐assisted selection is designed to maximize total net merit rather than the genetic response of the individual index trait as in the case of single‐trait MAS. Therefore, it is not economical to identify the QTL of the low heritability traits for the improvement of total net merit. The efficient, cost‐effective selection strategy is to identify the QTL of the moderate or high heritability traits of the QTL‐assisted selection index to facilitate total economic returns. Detection of the QTL of the low h² traits for the QTL‐assisted index selection is justified when the low h² traits have high negative genetic correlation with the other index traits and/or when both economic weights and genetic variances of the low h² traits are larger as compared to the other index traits of higher h². This study deals with theoretical efficiency of QTL‐assisted selection, but the same principle applies to SNP‐based genomic selection when the proportion of the genetic variance ‘explained by the identified QTLs’ in this study is replaced by ‘explained by SNPs’.     

Digestive Tract Anatomy of Norwegian Sheep: Difference Between Breeds

Data on 216,428 Danish Red, 798,152 Danish Friesian and 232,953 Danish Jersey cows were used to estimate phenotypic and genetic parameters for actual and production‐corrected survival traits and for milk production. Genetic effects of imported breeds were also estimated. Phenotypic trends in days in milk were similar for Danish Red and Danish Friesian, and showed influences of the milk quota system, whereas Danish Jersey showed a continuous downwards trend. Significant additive and non‐additive effects due to imported breeds were found. Heritabilities differed between breeds, ranging from 0.072 to 0.122 for actual continuous lifetime traits, and from 0.048 to 0.076 for production‐corrected continuous lifetime traits. Binary stayability traits showed lower heritability. Genetic correlations between milk production and actual or production‐corrected days in milk were 0.63 and 0.31 respectively. Genetic correlations between binary stayabilities and continuous lifetime traits were high (>0.78), which indicates that stayabilities can be used as early predictors of the lifetime traits.     

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.