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.

Inbreeding and pedigree analysis of the European red dairy cattle.

BACKGROUND: Red dairy cattle breeds have an important role in the European dairy sector because of their functional characteristics and good health. Extensive pedigree information is available for these breeds and provides a unique opportunity to examine their population structure, such as effective population size, depth of the pedigree, and effective number of founders and ancestors, and inbreeding levels. Animals with the highest genetic contributions were identified. Pedigree data included 9,073,403 animals that were born between 1900 and 2019 from Denmark, Finland, Germany, Latvia, Lithuania, the Netherlands, Norway, Poland, and Sweden, and covered 32 breeds. The numerically largest breeds were Red Dairy Cattle and Meuse-Rhine-Yssel. RESULTS: The deepest average complete generation equivalent (9.39) was found for Red Dairy Cattle in 2017. Mean pedigree completeness ranged from 0.6 for Finncattle to 7.51 for Red Dairy Cattle. An effective population size of 166 animals was estimated for the total pedigree and ranged from 35 (Rotes Höhenvieh) to 226 (Red Dairy Cattle). Average generation intervals were between 5 and 7 years. The mean inbreeding coefficient for animals born between 1960 and 2018 was 1.5%, with the highest inbreeding coefficients observed for Traditional Angler (4.2%) and Rotes Höhenvieh (4.1%). The most influential animal was a Dutch Meuse-Rhine-Yssel bull born in 1960. The mean inbreeding level for animals born between 2016 and 2018 was 2% and highest for the Meuse-Rhine-Yssel (4.64%) and Rotes Hohenvieh breeds (3.80%). CONCLUSIONS: We provide the first detailed analysis of the genetic diversity and inbreeding levels of the European red dairy cattle breeds. Rotes Höhenvieh and Traditional Angler have high inbreeding levels and are either close to or below the minimal recommended effective population size, thus it is necessary to implement tools to monitor the selection process in order to control inbreeding in these breeds. Red Dairy Cattle, Vorderwälder, Swedish Polled and Hinterwälder hold more genetic diversity. Regarding the Meuse-Rhine-Yssel breed, given its decreased population size, increased inbreeding and low effective population size, we recommend implementation of a breeding program to prevent further loss in its genetic diversity.

Identification of two new recessive MC1R alleles in red-coloured Evolèner cattle and other breeds.

Sequence variations in the melanocortin-1 receptor (MC1R) gene are associated with melanism in different animal species. Six functionally relevant alleles have been described in cattle to date. In a hypothesis-free approach we performed a genome-wide allelic association study with black, red and wild-coloured cattle of three Alpine cattle breeds (Eringer, Evolèner and Valdostana), revealing a single significant association signal close to the MC1R gene. We searched for candidate causative variants by sequencing the entire coding sequence and identified two novel protein-changing variants. We propose designating the mutant alleles at MC1R:c.424C>T as ev1 and at MC1R:c.263G>A as ev2 . Both affect conserved amino acid residues in functionally important transmembrane domains (p.Arg142Cys and p.Ser88Asn). Both alleles segregate predominantly in the Swiss Evolèner breed. They occur in other European cattle breeds such as Abondance and Rotes Höhenvieh as well. We observed almost perfect association between the MC1R genotypes and the coat colour phenotype in a cohort of 513 black, red and wild-coloured cattle. Animals carrying two copies of MC1R loss-of-function alleles or that were compound heterozygous for e, ev1 , or ev2 have a red to dark red (chestnut-like red) coat colour. These findings expand the spectrum of causal MC1R variants causing recessive red in cattle.

Development of a breeding program for improving the milk yield performance of Butana cattle under smallholder production conditions using a stochastic simulation approach.

Butana is one of the local dairy cattle breeds of Sudan commonly kept by smallholder producers. This breed has been strongly promoted to advance the dairy production sector in the country. The main problem, however, is the lack of a systematic breeding program that involves smallholder producers. The aim of the current study was to identify the most promising design for a breeding program to improve the milk yield performance of Butana cattle under smallholder production conditions. In total, 3 breeding scenarios, including (1) the use of farm bulls, (2) the use of village bulls, and (3) the rotational use of village bulls within village groups, were simulated using a stochastic simulation approach. For each breeding scenario, 3 selection methods for bulls were considered, namely random mating, phenotypic selection, and selection based on estimated breeding value (EBV). The results showed that no genetic gain was realized with random mating in all breeding scenarios. In the farm bull breeding scenario, annual genetic gain (standard deviation units) ranged from 0.01 to 0.19 (phenotypic selection) and from 0.01 to 0.39 (selection based on EBV). In the village bull breeding scenarios, the annual genetic gain ranged from 0.01 to 0.21 (phenotypic selection) and 0.01 to 0.45 (selection based on EBV). The lowest genetic gain was realized for the rotational use of village bulls among villages within groups. Through the rotational use of village bulls, however, a higher genetic variance was maintained than in the farm and village bull breeding scenarios. We concluded that a village bull breeding program with selection based on EBV of young bulls was the most promising breeding design for achieving the breeding goal. Further studies are needed to assess the organizational feasibility of such a breeding program to ensure the participation of smallholder producers and its sustainability.

Short- and long-term consequences of collaboration between Northern European Red dairy and dual-purpose cattle.

In Northern European countries, a great variety of Red cattle populations exists which can be broadly categorized in two groups: specialized dairy and dual-purpose breeds. Collaboration between these breeds (i.e. the exchange of sires across breeds) can be beneficial but is limited so far. The aim of this study was to demonstrate and evaluate consequences of collaboration between Red breeds using stochastic simulations. Two breeding lines (dairy type and dual purpose) were simulated. As a special aspect of this study, differences in genetic levels of breeding traits (milk production, beef production, mastitis resistance, fertility, feed efficiency) have been taken into account. Various scenarios were investigated where across-breed selection was either restricted or allowed and with different correlations between breeding goals in the two lines. The results of this study were influenced by the different genetic levels in breeding traits only in the first years of simulation. In the long run, the breed differences did not affect the degree of collaboration between lines. When the correlation between breeding goals was close to unity, the selection of external bulls was highly beneficial in terms of genetic gain and total monetary gain. Additionally, the lowest rate of inbreeding was found in that case. With decreasing correlations between environments, degree of cooperation between lines rapidly terminated and lines operated individually. In last years of simulation, cooperation was only found when the correlation between breeding goals was close to unity. From a long-term perspective, the exchange of breeding sires across lines also caused negative effects. In the dual-purpose line, deterioration of genetic gain in mastitis resistance and fertility was observed. Additionally, breeding lines genetically converged, which decreased genetic diversity. Collectively, short-term benefits and long-term negative effects have to be reconciled if collaboration between Red breeds in Northern Europe is to be pursued.

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.

Exploration of production conditions: a step towards the development of a community-based breeding program for Butana cattle.

In Sudan, many Butana cattle farmers practice indiscriminate crossbreeding to improve the milk yield performance of cows, as organized breeding programs are lacking. Objectives of this study were to identify the current production conditions of Butana cattle and to determine farmers' production objectives and trait preferences using a field survey. The overall aim was to explore the possibility of establishing a community-based breeding program for the genetic improvement of the breed. A semi-structured questionnaire and field visits were used to collect data from 202 Butana cattle owners. Data were analyzed using chi-squared test, multiple response analysis, and binary logistic regression. Our results showed that Butana cattle farmers mainly raised their animals for milk production. On a five-point scale (5 = most important), milk yield (4.6 ± 0.05), growth performance (4.0 ± 0.07), and lactation length (3.9 ± 0.08) were highly preferred for future development of the breed. One-third of the farmers kept crossbred cattle with on average 4 crossbred animals per herd. About two-thirds of respondents were willing to adopt crossbreeding using exotic breeds to increase milk performance and about the same proportion were willing to exchange breeding bulls and establish farmers' associations. None of the respondents kept written performance records. However, educated farmers were more likely to adopt record keeping. Farmers' willingness to engage in associations could be useful for the establishment of a community-based breeding program. Based on the current farmers' production objectives, the future breeding program should emphasize increasing milk production of the Butana cattle by using improved Butana bulls in village herds.

The benefit of native uniqueness in a local red cattle breed from Northern Germany.

During last decades, native uniqueness decreased in local livestock breeds due to the introgression of high-yielding breeds. Recovery of native uniqueness became important because of conservation aspects regarding native genetic diversity and native traits. Thereby the expectation exists, that the relation between native uniqueness and genetic gain is contradictory. The aim of this study was to explore the influence of native uniqueness on performance traits and the total merit index in a local red cattle breed from Northern Germany. Data contained a pedigree file of 178,255 Red Dual-Purpose cattle, 809 target genotypes and 3,581 reference genotypes from introgressed breeds. Native genetic contributions were tested for correlation with performance traits of milk yield, longevity, foundation, somatic cells, fertility and maternal calving and the total merit index. The study revealed that native uniqueness is favourably related to longevity (0.16), foundation (0.23), and somatic cells (0.08), and the total merit index (0.10). Selection on native uniqueness could probably lead to an increased longevity, udder health and genetic gain of the Red Dual-Purpose cattle. Moreover, it was shown that the Red Dual-Purpose cattle was not upgraded through introgression of high-yielding breeds.

Presence of keel bone damage in laying hens, pullets and roosters of local chicken breeds.

In commercial laying hens, keel bone damage (KBD) is a severe health and welfare problem leading to pain, reduced mobility and decreased laying performance. Flocks of all production systems and hybrid lines can be affected. KBD is a multifactorial welfare issue and, among other factors, associated with a high laying performance which negatively affects the calcium deposit in the medullary bones. Therefore, mature hens of local breeds with much lower egg production than commercial hybrids may be expected to show less or even no keel bone damage. This study evaluates (i) the prevalence of KBD in local breeds, (ii) the difference in type and level of damages, and (iii) if roosters and pullets are also affected. In total, we palpated 343 mature hens, 40 pullets, and 18 roosters of 13 different local breeds and one commercial hybrid. The animals were kept on eight different farms in free-range or floor-housing systems. Our results showed that on average 44.2% of mature hens per local breed were affected by KBD (range: 11.1%-84.7%). We found deviation of less than 1 cm in 26.9%, deviations of more than 1 cm in 6.4% and palpable fractures in 23.8% of the mature hens of local breeds. The tip was damaged in 23.6% of the mature hens. Also, pullets and roosters were affected by KBD. Finally, we found that KBD also occurs in local breeds. Therefore, we conclude that even the low laying performance of local breeds does not prevent them from the occurrence of KBD.KBD in local breeds may rather be associated with genetics (breed) as well as management and housing. Thus, breeders of local breeds should include bone health as a selection trait. Owners of local breeds should also pay attention to the condition of the keel and ought to be trained about preventive measures.

Performance, carcass quality and meat quality of the endangered German Angler Saddleback pig.

The Angler Saddleback pig is an endangered local breed originating from Germany. The breed is said to have low demands in terms of husbandry and feeding, and an excellent meat quality. To date, there is a lack of more recent scientific investigations of the breed. Therefore, 58 Angler Saddleback pigs were fattened in two consecutive trials whereby performance, carcass quality and meat quality were assessed. At an average age of 324 days, the pigs reached an average final live weight of 143 kg, an intramuscular fat (IMF) content of 2.6%, a lean meat percentage of 47% and a backfat thickness of 38 mm. A significant influence of the independent variables "breeder" and "age at the end of fattening" on the majority of target variables was found. Furthermore, IMF as well as pH value 45 minutes post mortem was significantly influenced by sex. These results give a current overview of the phenotypic characteristics of this endangered breed. It is shown that the slower growing Angler Saddleback breed may need alternative marketing concepts for its meat and meat products. Additionally, further research is necessary to clarify the reasons for the high phenotypic variation within this breed.

An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds.

Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds.

Genetic diversity and the application of runs of homozygosity-based methods for inbreeding estimation in German White-headed Mutton sheep.

The German White-headed Mutton (GWM) sheep is a monitoring population believed to have been improved through crosses with other breeds, e.g., Texel (TXL) and French Berrichone du Cher (BDC). The primary aim of the study was to analyse genetic diversity and breed composition of GWM sheep. Furthermore, different measures of computing inbreeding from the runs of homozygosity (ROH) were investigated. Data for GWM consisted of pedigree information on 19,000 animals and 40,753 quality filtered SNPs on 46 individuals. Additionally, publicly available genotype data on 209 individuals belonging to nine sheep breeds were included in the analysis. Due to evenness of SNPs spacing and proportionality of the number of SNPs in each autosome to autosome length, a high correlation (rp = 0.99) was found between genomic inbreeding coefficients computed based on the length of ROH (FROH_L) and those computed relative to the number of SNPs in ROH (FROH_N). Total inbreeding was partitioned into values for individual chromosomes revealing the highest levels of inbreeding on chromosomes 1, 2 and 3. Correlations between the ROH-based inbreeding measures and pedigree inbreeding reached 0.82. The observed heterozygosity estimate in GWM was high (0.39), however, the breed suffered low level of effective population size (~50) from a genomic viewpoint. Moreover, effective number of founders (186), and effective number of ancestors (144) implied disequilibrium of founder contribution and a genetic bottleneck in the breed. Multidimensional scaling and network visualisation analyses revealed close connectedness of GWM to BDC and German Texel (GTX). A model-based admixture analysis consistently indicated the flow of genes from other breeds, particularly BDC to GWM. Our analyses highlight the mixed genetic background of GWM sheep and furthermore, suggest a close monitoring of the breed to consolidate its genetic diversity while averting further reduction in the effective population size.

A Review of Genomic Models for the Analysis of Livestock Crossbred Data.

Livestock breeding has shifted during the past decade toward genomic selection. For the estimation of breeding values in purebred breeding schemes, genomic best linear unbiased prediction has become the method of choice. Systematic crossbreeding with the aim to utilize heterosis and breed complementary effects is widely used in livestock breeding, especially in pig and poultry breeding. The goal is to improve the performance of the crossbred animals. Due to genotype-by-environment interactions, imperfect linkage disequilibrium, and the existence of dominance and imprinting, purebred and crossbred performances are not perfectly correlated. Hence, more complex genomic models are required for crossbred populations. This study reviews and compares such models. Compared to purebred genomic models, the reviewed models were of much higher complexity due to the inclusion of dominance effects, breed-specific effects, imprinting effects, and the joint evaluation of purebred and crossbred performance data. With the model assessment work conducted until now, it is not possible to come to a clear recommendation as to which existing method is most suitable for a specific breeding program and a specific genetic trait architecture. Since it is expected that a superior method includes all the different genetic effects in a single model, a dominance model with imprinting and breed-specific SNP effects is proposed. Further progress could be made by assuming realistic covariance structures between the genetic effects of the different breeding lines, and by using larger marker panels and mixture distributions for the SNP effects.

Runs of Homozygosity and NetView analyses provide new insight into the genome-wide diversity and admixture of three German cattle breeds.

Angler (RVA) and Red-and-White dual-purpose (RDN) cattle were in the past decades crossed with influential Red Holstein (RH) sires. However, genome-wide diversity studies in these breeds are lacking. The objective of the present study was to elucidate the genome-wide diversity and population structure of the three German cattle breeds. Using 40,851 single nucleotide polymorphism markers scored in 337 individuals, runs of homozygosity (ROH) were analysed in each breed. Clustering and a high-resolution network visualisation analyses were performed on an extended dataset that included 11 additional (outgroup) breeds. Genetic diversity levels were high with observed heterozygosity above 0.35 in all three breeds. Only RVA had a recent past effective population size (Ne) estimate above 100 at 5 generations ago. ROH length distribution followed a similar pattern across breeds and the majority of ROH were found in the length class of >5 to 10 Mb. Estimates of average inbreeding calculated from ROH (FROH) were 0.021 (RVA), 0.045 (RDN) and 0.053 (RH). Moderate to high positive correlations were found between FROH and pedigree inbreeding (FPED) and between FROH and inbreeding derived from the excess of homozygosity (FHOM), while the intercept of the regression of FROH on FPED was above zero. The population structure analysis showed strong evidence of admixture between RVA and RH. Introgression of RDN with RH genes was minimally detected and for the first time, the study uncovered Norwegian Red Cattle ancestry in RVA. Highly heterogeneous genetic background was found for RVA and RH and as expected, the breeds of the extended dataset effectively differentiated mostly based on geographical origin, validating our findings. The results of this study confirm the impact of RH sires on RVA and RDN populations. Furthermore, a close monitoring is suggested to curb further reduction of Ne in the breeds.