Genetic evaluations and genome-wide association studies for specific digital dermatitis diagnoses in dairy cows considering genotype × housing system interactions.

The present study aimed to use detailed phenotyping for the claw disorder digital dermatitis (DD) considering specific DD stages in 2 housing systems (conventional cubicle barns [CON] and compost-bedded pack barns [CBPB]) to infer possible genotype × housing system interactions. The DD stages included 2,980 observations for the 3 traits DD-sick, DD-acute, and DD-chronic from 1,311 Holstein-Friesian and 399 Fleckvieh-Simmental cows. Selection of the 5 CBPB and 5 CON herds was based on a specific protocol to achieve a high level of herd similarity with regard to climate, feeding, milking system, and location, but with pronounced housing-system differences. Five other farms had a "mixed system" with 2 subherds, one representing CBPB and the other one CON. The CBPB system was represented by 899 cows (1,530 observations), and 811 cows (1,450 observations) represented the CON system. The average disease prevalence was 20.47% for DD-sick, 13.88% for DD-acute, and 5.34% for DD-chronic, with a higher prevalence in CON than in CBPB. After quality control of 50K genotypes, 38,495 SNPs from 926 cows remained for the ongoing genomic analyses. Genetic parameters for DD-sick, DD-acute, and DD-chronic were estimated by applying single-step approaches for single-trait repeatability animal models considering the whole dataset, and separately for the CON and CBPB subsets. Genetic correlations between same DD traits from different housing systems, and between DD-sick, DD-chronic, and DD-acute, were estimated via bivariate animal models. Heritabilities based on the whole dataset were 0.16 for DD-sick, 0.14 for DD-acute, and 0.11 for DD-chronic. A slight increase of heritabilities and genetic variances was observed in CON compared with the "well-being" CBPB system, indicating a stronger genetic differentiation of diseases in a more challenging environment. Genetic correlations between same DD traits recorded in CON or CBPB were close to 0.80, disproving obvious genotype × housing system interactions. Genetic correlations among DD-sick, DD-acute and DD-chronic ranged from 0.58 to 0.81. SNP main effects and SNP × housing system interaction effects were estimated simultaneously via GWAS, considering only the phenotypes from genotyped cows. Ongoing annotations of potential candidate genes focused on chromosomal segments 100 kb upstream and downstream from the significantly associated candidate SNP. GWAS for main effects indicated heterogeneous Manhattan plots especially for DD-acute and DD-chronic, indicating particularities in disease pathogenesis. Nevertheless, a few shared annotated potential candidate genes, that is, METTL25, AFF3, PRKG1, and TENM4 for DD-sick and DD-acute, were identified. These genes have direct or indirect effects on disease resistance or immunology. For the SNP × housing system interaction, the annotated genes ASXL1 and NOL4L on BTA 13 were relevant for DD-sick and DD-acute. Overall, the very similar genetic parameters for the same traits in different environments and negligible genotype × housing system interactions indicate only minor effects on genetic evaluations for DD due to housing-system particularities.

Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle.

When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI's database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists.

Genetic evaluations for endangered dual-purpose German Black Pied cattle using 50K SNPs, a breed-specific 200K chip, and whole-genome sequencing.

Genetic evaluations of local cattle breeds are hampered due to small reference groups or biased due to the utilization of SNP effects estimated in other large populations. Against this background, there is a lack of studies addressing the possible advantage of whole-genome sequences (WGS) or consideration of specific variants from WGS data in genomic predictions for local breeds with small population size. Consequently, the aim of this study was to compare genetic parameters and accuracies of genomic estimated breeding values (GEBV) for 305-d production traits, fat-to protein ratio (FPR), and somatic cell score (SCS) at the first test date after calving and confirmation traits of the endangered German Black Pied cattle (DSN) breed using 4 different marker panels: (1) the commercial 50K Illumina BovineSNP50 BeadChip, (2) a customized 200K chip designed for DSN (DSN200K) which considers the most important variants for DSN from WGS, (3) randomly generated 200K chips based on WGS data, and (4) a WGS panel. The same number of animals was considered for all marker panel analyses (i.e., 1,811 genotyped or sequenced cows for conformation traits, 2,383 cows for lactation production traits, and 2,420 cows for FPR and SCS). Mixed models for the estimation of genetic parameters directly included the respective genomic relationship matrix from the different marker panels plus the trait-specific fixed effects. For the calculation of GEBV accuracies, we applied repeated random subsampling validation. In the process of separate cross-validations per trait, we created a validation set including 20% of cows with masked phenotypes, and a training set comprising 80% of the cows. The cows were selected randomly in a procedure with 10 replicates considering replacements in the different scenarios. The accuracy was defined as the correlation between the direct GEBV and the phenotypes with subtracted corresponding fixed effects for the cows in the validation set. For FPR and SCS, as well as for lactation production traits, heritabilities were largest based on WGS data, but the increase compared with the 50K or DSN200K applications was quite small in the range from 0.01 to 0.03. Also, for most of the conformation traits, heritabilities were largest based on WGS and DSN200K data, but the increase was in the range of the corresponding standard error. Accordingly, GEBV accuracies for most of the studied traits were highest based on WGS data or when utilizing the DSN200K chip, but the accuracy differences across the marker panels were quite small and nonsignificant. In conclusion, WGS data and the DSN200K chip only contributed to minor improvements in genomic predictions, still justifying the use of the commercial 50K chip. Nevertheless, WGS and the 200KDSN chip harbor breed-specific variants, which are valuable for studying causal genetic mechanisms in the endangered DSN population.

Genetic parameters for linear conformation, stayability, performance and reproduction traits in German local Swabian-Hall landrace sows.

Improvements of longevity in sows are of overriding importance from an animal welfare as well as from an economic perspective, also in the local Swabian-Hall Landrace (SHL) breed. Consequently, the aim of the present study was a detailed assessment of linear conformation traits in the context of early predictions of sow stayability and to infer genetic (co)variance components between conformation traits with reproduction and performance traits. In this regard, we implemented a linear 9-point scoring system for conformation traits reflecting the body morphology and feet and leg characteristics in gilts. Linear conformation trait scoring included body length (BLEN), body height (BHEI), hind leg angularity (HLANG), hind leg pastern (HLPAS), hind cannon bone strength (HCBS), hind leg position (HLPOS), front leg position (FLPOS), claw length (CLEN) and muscling (MUSC) from 6042 SHL gilts before first insemination at the age of 180-200 days. For the same gilts, performance traits included average daily gain (ADG) and back fat thickness (BF) measured via ultrasound, reproduction traits included the number of piglets born alive (NBA) and the number of piglets weaned (NWEAN), and stayability was a binary trait reflecting sow survival after parity 2 (STAY_12), 3 (STAY_13) and 4 (STAY_14). For the estimation of variance components and heritabilities, single-trait linear animal models were defined for conformation, performance and reproduction traits, and single-trait generalized linear mixed models with a logit link function for binary stayability traits. Genetic covariances and correlations were inferred in series of bivariate runs for all combinations of conformation and remaining traits. The distribution of the assigned conformation scores reflected a Gaussian distribution, but a large fraction of records was assigned to the intermediate score classes 4, 5 and 6. Accordingly, the restricted utilization of the 9-point scale might explain the small genetic variances and small heritabilities for feet and leg traits in the range from 0.06 to 0.17. Heritabilities were larger for the linear traits reflecting body morphology, i.e., for BLEN (0.21) and BHEI (0.20). For conformation traits, the common litter environment explained up to 17% of the phenotypic trait variation. Genetic and especially phenotypic correlations between linear conformation traits with the reproduction traits NBA and NWEAN were close to zero. Heritabilities for STAY_12, STAY_13 and STAY_14 were 0.08, 0.07 and 0.05, respectively. Moderate genetic relationships were estimated between STAY_14 with some conformation traits. Especially high scores for BHEI and BLEN (i.e., long and large gilts) implied a decline in STAY_14 genetically (rg  = -0.24 and -0.53, respectively). Moderate genetic correlations were estimated between HLANG with STAY_14 (0.28), and between HCBS with STAY_12 (0.23). For most of the conformation traits with intermediate optimum, genetic correlations with STAY were close to zero, indicating improved longevity for gilts representing the population average with scores 4, 5 or 6, and suggesting the development of appropriate selection indices in this regard.

Multiple-trait and structural equation modelling approaches to infer genetic relationships between tail length and weight traits in Merinoland sheep.

Tail docking is routinely conducted in long-tailed sheep breeds to prevent flystrike infections, but it is not in agreement with legal guidelines and animal welfare issues. Selection on short tails is a sustainable alternative in this regard, but side effects on other breeding goal traits are unclear. In consequence, the present study aimed to estimate genetic parameters for tail length (TL) at birth, birth weight (BW), weaning weight (WW) and postweaning weight (PWW) at the slaughtering date considering single-trait (STM), multiple-trait (MTM) and structural equation models (SEM) with different random effects, and accordingly, different covariance structures. The SEM considered time-lagged recursive relationships among response variables in three different pathways. The first path pertained to the effect of TL on WW and of WW on PWW. The second path reflected the effect of BW on WW and of WW on PWW. The third path was the recursive effect of TL on PWW. The phenotypic data consisted of 2803 records for TL, 13,042 records for BW, 1556 records for WW and 3986 records for PWW from Merinoland lambs. Lambs were born in the period from 1995 to 2021 and kept at the university Gießen research station, Germany, with their naturally long tails. Genetic statistical model evaluation based on Bayesian and Akaike's information criteria suggested models simultaneously considering direct genetic, maternal genetic and maternal permanent environmental effects and respective covariances. For statistical models including the same random effects and covariance structures, SEM were superior over MTM. The direct heritability for TL from the best-fitting STM was 0.60 ± 0.08, indicating the potential for genetic reduction of tail length within a few generations. For growth traits, the direct heritabilities ranged from 0.16 ± 0.03 for BW to 0.31 ± 0.09 for PWW. The maternal heritabilities were 0.03 ± 0.03 for TL, 0.12 ± 0.02 for BW, 0.04 ± 0.03 for WW and 0.07 ± 0.03 for PWW, reflecting small, but the non-significant influence of uterine characteristics on the tail development. The direct genetic correlations between TL and all weight traits were positive and very similar to MTM and SEM but reflected antagonistic genetic relationships from a breeding perspective. Oppositely, the structural equation coefficients reflecting trait associations phenotypically were negative (favourable) for the time-lagged effects of TL on WW and on PWW. As an explanation, lambs with long and woolly tails have an increased risk for contamination with dirt and dust causing infections, which in turn impairs the body weight development. In conclusion, breeding on short tails should consider trait-associated environmental risk factors, for example, disease susceptibility, which can be mimicked via SEM approaches.

Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis in German Holstein cattle.

Domestication and selection significantly changed phenotypic and behavioural traits in modern domestic animals. In this study, to identify the genomic regions associated with mastitis, genomic data of German Holstein dairy cattle were analysed. The samples were genotyped using the Bovine 50 K SNP chip. For each defined healthy and sick group, 133 samples from 13,276 genotyped dairy cows were selected based on mastitis random residual effects. Grouping was done to infer selection signatures based on XP-EHH statistic. The results revealed that for the top 0.01 percentile of the obtained XP-EHH values, five genomic regions on chromosomes 8, 11, 12, 14 and 26 of the control group, and four regions on chromosomes 3, 4 (two regions) and 22 of the case group, have been under selection. Also, consideration of the top 0.1 percentile of the XP-EHH values, clarified 21 and 15 selective sweeps in the control and case group, respectively. This study identified some genomic regions containing potential candidate genes associated with resistance and susceptibility to mastitis, immune system and inflammation, milk traits, udder morphology and different types of cancers. In addition, these regions overlap with some quantitative trait loci linked to clinical mastitis, immunoglobulin levels, somatic cell score, udder traits, milk fat and protein, milk yield, milking speed and veterinary treatments. It is noteworthy that we found two regions in the healthy group (on chromosomes 12 and 14) with strong signals, which were not described previously. It is likely that future research could link these identified genomic regions to mastitis. The results of the current study contribute to the identification of causal mutations, genomic regions and genes affecting mastitis incidence in dairy cows.

Novel Insights to Assess Climate Resilience in Goats Using a Holistic Approach of Skin-Based Advanced NGS Technologies.

A novel study was conducted to elucidate heat-stress responses on a number of hair- and skin-based traits in two indigenous goat breeds using a holistic approach that considered a number of phenotypic and genomic variables. The two goat breeds, Kanni Aadu and Kodi Aadu, were subjected to a simulated heat-stress study using the climate chambers. Four groups consisting of six goats each (KAC, Kaani Aadu control; KAH, Kanni Aadu heat stress; KOC, Kodi Aadu control; and KOH, Kodi Aadu heat stress) were considered for the study. The impact of heat stress on caprine skin tissue along with a comparative assessment of the thermal resilience of the two goat breeds was assessed. The variables considered were hair characteristics, hair cortisol, hair follicle quantitative PCR (qPCR), sweating (sweating rate and active sweat gland measurement), skin histometry, skin-surface infrared thermography (IRT), skin 16S rRNA V3-V4 metagenomics, skin transcriptomics, and skin bisulfite sequencing. Heat stress significantly influenced the hair fiber characteristics (fiber length) and hair follicle qPCR profile (Heat-shock protein 70 (HSP70), HSP90, and HSP110). Significantly higher sweating rate, activated sweat gland number, skin epithelium, and sweat gland number (histometry) were observed in heat stressed goats. The skin microbiota was also observed to be significantly altered due to heat stress, with a relatively higher alteration being noticed in Kanni Aadu goats than in Kodi Aadi goats. Furthermore, the transcriptomics and epigenetics analysis also pointed towards the significant impact of heat stress at the cellular and molecular levels in caprine skin tissue. The higher proportion of differentially expressed genes (DEGs) along with higher differentially methylated regions (DMRs) in Kanni Aadu goats due to heat stress when compared to Kodi Aadu goats pointed towards the better resilience of the latter breed. A number of established skin, adaptation, and immune-response genes were also observed to be significantly expressed/methylated. Additionally, the influence of heat stress at the genomic level was also predicted to result in significant functional alterations. This novel study thereby highlights the impact of heat stress on the caprine skin tissue and also the difference in thermal resilience exhibited by the two indigenous goat breeds, with Kodi Aadu goats being more resilient.

Urbanisation threats to dairy cattle health: Insights from Greater Bengaluru, India.

Complex urbanisation dynamics, on the one hand, create a high demand for animal products, and on the other hand put enormous pressure on arable land with negative consequences for animal feed production. To explore the impact of accelerated urbanisation on dairy cattle health in urban farming systems, 151 farmers from different parts of the Greater Bengaluru metropolitan area in India were individually interviewed on aspects addressing cattle management and cattle health. In addition, 97 samples of forages from the shores of 10 different lakes, and vegetable leftovers used in cattle feeding were collected for nutritional analysis. Along with the use of cultivated forages, crop residues, and concentrate feed, 47% and 77% of the farmers occasionally or frequently used lake fodder and food leftovers, respectively. Nutritionally, lake fodder corresponded to high-quality pasture vegetation, but 43% of the samples contained toxic heavy metals such as arsenic, cadmium, chromium, and lead above official critical threshold levels. Therefore, lake fodder may affect cows' health if consumed regularly; however, heavy metal concentrations varied between lakes (P < 0.05), but not between fodder types (P > 0.05). Although 60% of the interviewed farmers believed that their cows were in good health, logit model applications revealed that insufficient drinking water supply and the use of lake fodder negatively impacted cattle health (P < 0.05). While it remains unknown if regular feeding of lake fodder results in heavy metal accumulation in animal products, farmers and farm advisors must address this and other urbanization-related challenges to protect cattle health.

Molecular matched targeted therapies for primary brain tumors-a single center retrospective analysis.

PURPOSE: Molecular diagnostics including next generation gene sequencing are increasingly used to determine options for individualized therapies in brain tumor patients. We aimed to evaluate the decision-making process of molecular targeted therapies and analyze data on tolerability as well as signals for efficacy. METHODS: Via retrospective analysis, we identified primary brain tumor patients who were treated off-label with a targeted therapy at the University Hospital Frankfurt, Goethe University. We analyzed which types of molecular alterations were utilized to guide molecular off-label therapies and the diagnostic procedures for their assessment during the period from 2008 to 2021. Data on tolerability and outcomes were collected. RESULTS: 413 off-label therapies were identified with an increasing annual number for the interval after 2016. 37 interventions (9%) were targeted therapies based on molecular markers. Glioma and meningioma were the most frequent entities treated with molecular matched targeted therapies. Rare entities comprised e.g. medulloblastoma and papillary craniopharyngeoma. Molecular targeted approaches included checkpoint inhibitors, inhibitors of mTOR, FGFR, ALK, MET, ROS1, PIK3CA, CDK4/6, BRAF/MEK and PARP. Responses in the first follow-up MRI were partial response (13.5%), stable disease (29.7%) and progressive disease (46.0%). There were no new safety signals. Adverse events with fatal outcome (CTCAE grade 5) were not observed. Only, two patients discontinued treatment due to side effects. Median progression-free and overall survival were 9.1/18 months in patients with at least stable disease, and 1.8/3.6 months in those with progressive disease at the first follow-up MRI. CONCLUSION: A broad range of actionable alterations was targeted with available molecular therapeutics. However, efficacy was largely observed in entities with paradigmatic oncogenic drivers, in particular with BRAF mutations. Further research on biomarker-informed molecular matched therapies is urgently necessary.

Genomic loci and genetic parameters for uterine diseases in first-parity Holstein cows and associations with milk production and fertility.

Based on the clinical stage (e.g., vaginal discharge) and bacterial species, several forms of uterine diseases (UD) exist and can be classified as different traits [i.e., different stages of endometritis (EM) and metritis (MET)], which may differ in their genetic background and causal physiological mechanisms. Consequently, the present study aimed to study (1) the effect of UD on 305-d lactation and fertility, (2) the estimation of heritabilities for UD traits using pedigree- and SNP-based relationships, and (3) genome-wide associations to detect significant SNP markers and to infer candidate genes for UD traits. The data set contained herd manager and veterinarian recorded UD traits of 14,810 first-lactating genotyped Holstein cows from 63 large-scale contract herds. Binary defined UD traits (healthy or diseased) according to the clinical stage were endometritis catarrhalis (EM I), endometritis mucopurulenta (EM II), endometritis purulenta (EM III), pyometra (EM IV), endometritis (EM_SOD; superordinate diagnosis = no specific clinical stage defined), and MET. The binary defined trait UDall included all EM and MET diagnoses. The prevalence of UDall was 26.7%. The effect of UD on 305-d lactation and fertility was estimated via linear and generalized linear mixed models. We applied linear single-trait animal models and threshold models to estimate pedigree- and SNP-based heritabilities for UD traits, and bivariate linear models for genetic correlation estimations between UDall with 305-d lactation and fertility traits. A diagnosis for UDall had significant unfavorable effects on the female fertility traits calving interval, interval from calving to first service, days open, and nonreturn rate after 90 d, but was unrelated to 305-d lactation records for production traits milk yield, protein yield, and fat yield. Heritabilities for UDall and EM stages were close to zero, displaying maximal values of 0.05 for pedigree and 0.07 for SNP-based relationship matrices. For MET, pedigree- and SNP-based heritabilities were <0.001 and 0.07, respectively. Genetic correlations ranged from 0.20 to 0.31 between UDall with 305-d milk, protein, and fat yield, and from 0.17 to 0.40 with fertility traits. The GWAS revealed 5 SNP on bovine chromosomes (BTA) 1, 8, 10, 23 for UDall, 5 SNP on BTA 26 for EM I, 1 SNP on BTA 19 for EM II, 4 SNP on BTA 2, 18, 20, 25 for EM III, and 4 SNP on BTA 4, 16, 20 for EM IV above the significance threshold. For EM_SOD, we identified 15 significantly associated SNP on 4 chromosomes, and 4 significant SNP on BTA 3, 20, 22, 28 for MET. Marker associations for UD traits were annotated to 24 potential candidate genes using the ENSEMBL database. Six of these genes were previously reported to be involved in uterine defense mechanisms or in endometritis. Further detected genes contribute to immune response mechanisms during bacterial infections. Different SNP significantly influenced different UD stages, explaining the inter-individual variations in clinical severity of uterine infections.

Genomic analyses of claw disorders in Holstein cows: Genetic parameters, trait associations, and genome-wide associations considering interactions of SNP and heat stress.

The aim of the present study was an in-depth genomic analysis to understand the genomic mechanisms of the 3 claw disorders dermatitis digitalis (DD), interdigital hyperplasia (HYP), and sole ulcer (SU). In this regard, we estimated genetic parameters based on genomic relationship matrices, performed genome-wide association studies, annotated potential candidate genes, and inferred genetic associations with breeding goal traits considering the most important chromosomal segments. As a further novelty of this study, we inferred possible SNP × heat stress interactions for claw disorders. The study consisted of 17,264 first-lactation Holstein Friesian cows kept in 50 large-scale contract herds. The disease prevalence was 15.96, 2.36, and 8.20% for DD, HYP, and SU, respectively. The remaining breeding goal traits consisted of type traits of the feet and leg composite, female fertility, health traits, and 305-d production traits. The final genotype data set included 44,474 SNPs from the 17,264 genotyped cows. Heritabilities for DD, HYP, and SU were estimated in linear and threshold models considering the genomic relationship matrix (G matrix). Genetic correlations with breeding goal traits based on G were estimated in a series of bivariate linear models, which were verified via SNP effect correlations for specific chromosome segments (i.e., segments harboring potential candidate genes for DD, HYP, and SU). Genome-wide association studies were performed for all traits in a case-control design by applying a single SNP linear mixed model. Furthermore, for DD, HYP, and SU, we modeled SNP × heat stress interactions in genome-wide association studies. Single nucleotide polymorphism-based heritabilities were 0.04 and 0.08 for DD, 0.03 and 0.10 for SU, and 0.03 and 0.23 for HYP from linear and threshold models, respectively. The genetic correlations between DD, HYP, and SU with conformation traits from the feet and leg composite were positive throughout, indicating the value of indirect selection on conformation traits to improve claw health. Genetic correlations between DD, SU, and HYP with other breeding goal traits indicated impaired female fertility, impaired udder health status, and productivity decline of diseased cows. Genetic correlations among DD, SU, and HYP were moderate to large, indicating that different claw disorders have similar genetic mechanisms. Nevertheless, we identified disease-specific potential candidate genes, and genetic associations based on the surrounding SNPs partly differed from the genetic correlations. Especially for candidate genes contributing to 2 traits simultaneously, correlations based on SNP effects from the respective chromosome segment were close to 1 or to -1. In this regard, we annotated the candidate genes KRT33A and KRT33B for HYP and DD, KIF27 for HYP and calving to first insemination, and MAN1A1 for SU and the production traits. For SNP × heat stress interactions, we identified significant SNPs on BTA 2, 4, 5, 7, 8, 9, 13, 22, 25, and 28, and we annotated the potential candidate genes FSIP2, CLCN1, ADGRV1, DOP1A, THBD, and RHOBTB1. Results indicate gene-specific mechanisms of the claw disorders only in specific environments.

Phenotypic and genetic diversity of domestic yak (Bos grunniens) in high-altitude rangelands of Gilgit-Baltistan, Pakistan.

Due to climate change, irrigated agriculture may become restricted in the mountain valleys in northern Pakistan in the future. Hence, the importance of yak (Bos grunniens) keeping in the mountain ranges as risk-mitigating strategy for mountain dwellers will potentially increase. However, little is known about the current status of the domestic yak in this region. We therefore used phenotypic characteristics and 13 microsatellite loci to determine the phenotypic differences and the level of genetic differentiation between populations of six valleys. Larger body measures and partially different physical appearance were observed in Shimshal and Khaplu yaks, especially when compared with yaks in the Chapurson valley. Overall, the mean observed heterozygosity was similar to the mean expected heterozygosity. Average genetic diversity was highest in the Hopar population and lowest in the Haramosh population. A low FIS value indicated that individuals were less related than expected under a model of random mating. Three distinct genetic clusters were found for the six yak populations under study. Genetic distances were largest between Shimshal and Khaplu populations, and lowest between populations of Phandar and Hopar. It is concluded that yaks of Shimshal, Khaplu and Haramosh valleys were genetically distinct from yak populations in Chapurson, Hopar and Phandar valleys, indicating that the free-range conditions and pastoral yak rearing system in the region have preserved the underlying genetic diversity of the yak populations.

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN).

BACKGROUND: German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN's genetic diversity and to provide avenues for genetic improvement. RESULTS: Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. CONCLUSION: The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

A variance component estimation approach to infer associations between Mendelian polledness and quantitative production and female fertility traits in German Simmental cattle.

BACKGROUND: Managing beneficial Mendelian characteristics in dairy cattle breeding programs implies that the correlated genetic effects are considered to avoid possible adverse effects in selection processes. The Mendelian trait polledness in cattle is traditionally associated with the belief that the polled locus has unfavorable effects on breeding goal traits. This may be due to the inferior breeding values of former polled bulls and cows in cattle breeds, such as German Simmental, or to pleiotropic or linkage effects of the polled locus. METHODS: We focused on a variance component estimation approach that uses a marker-based numerator relationship matrix reflecting gametic relationships at the polled locus to test for direct pleiotropic or linked quantitative trait loci (QTL) effects of the polled locus on relevant traits. We applied the approach to performance, health, and female fertility traits in German Simmental cattle. RESULTS: Our results showed no evidence for any pleiotropic QTL effects of the polled locus on test-day production traits milk yield and fat percentage, on the mastitis indicator 'somatic cell score', and on several female fertility traits, i.e. 56 days non return rate, days open and days to first service. We detected a significant and unfavorable QTL effect accounting for 6.6% of the genetic variance for protein percentage only. CONCLUSIONS: Pleiotropy does not explain the lower breeding values and phenotypic inferiority of polled German Simmental sires and cows relative to the horned population in the breed. Thus, intensified selection in the polled population will contribute to increased selection response in breeding goal traits and genetic merit and will narrow the deficit in breeding values for production traits.

Microscopic differential cell count and specific mastitis pathogens in cow milk from compost-bedded pack barns and cubicle barns.

Compost bedded pack barns (compost) as a new free walk housing system favorably influence udder health due to improved animal welfare and lying comfort. On the other hand, unfavorable effects on udder health are possible, due to the open bedded pack and the associated larger bacterial content in moisture. For in-depth farming system comparisons, the present study aimed to evaluate the specific cell fractions and mastitis pathogens in milk from cows kept in compost and in conventional cubical barns (cubicle). For milk sample collection we used a repeated measurement data structure of 2,198 udder quarters from 537 Holstein cows kept in six herds (3 in compost and 3 in cubicle). Differential cell counting was conducted including lymphocytes, macrophages and polymorphonuclear leukocytes (PMN). Specific mastitis pathogens comprised major and minor pathogens. Mixed models were applied to infer environmental and cow associated effects on cell fractions and on prevalences for pathogen infections, with specific focus on system × lactation stage, system × milk yield and system × somatic cell count effects. The interaction between system and lactation stage showed significant differences (P < 0.01) between the systems. A significantly smaller number of bacteriologically positive quarters and lower prevalences for minor pathogens were detected in compost compared to cubicle. Least squares means for pathogen prevalences indicated a quite constant proportion of bacteriologically negative udder quarters across milk yield levels in compost, but a slight increase with increasing milk yield in cubicle. Cell fraction responses in both systems differed in relation to the overall bacteriological infection status and farming system particularities. In conclusion, different cell fractions and specific mastitis pathogens should be considered as an indicator for udder health in different production systems, taking into account cow associated factors (lactation stage, milk yield).

Across-generation effects of maternal heat stress during late gestation on production, female fertility and longevity traits in dairy cows.

This research paper focuses on time-lagged heat stress (HS) effects from an across-generation perspective. Temperature × humidity indexes (THI) from the last 8 weeks of pregnancy were associated with subsequent female offspring performances. The offspring dataset considered 172 905 Holstein dairy cows from calving years 2002-2013 from 1,968 herds, located in the German federal state of Hesse. Production traits included milk yield (MKG), protein percentage (PRO%), fat percentage (FAT%), somatic cell score (SCS) and milk urea nitrogen (MUN) from the first official test-day in first lactation. Female fertility traits were the non-return-rate after 56 d (NRR56) in heifers and the interval from calving to first insemination (ICFI) in first parity cows. Longevity traits were the length of productive life (LPL), lifetime productivity in milk yield (LTP-MKG) and milk yield per day of life (MKG-DL). The association analyzes for 10 traits combined with meteorological data from 8 single weeks before calving implied in total 80 different runs. THI ≥50 from all single 8 weeks before calving had unfavorably significant effects on FAT%, ICFI and LPL. Heat stress in terms of THI ≥60 from the last 3 weeks before calving impaired MKG. NRR56 decreased with increasing THI, as observed for all 6 weeks before calving. LTP-MKG and MKG-DL decreased due to high THI in the last 4 weeks before calving. Heat stress (THI ≥60) during late pregnancy had no significantly unfavorable impact on PRO% and MUN. Interestingly, SCS in offspring declined with increasing THI during late pregnancy. In conclusion, for most of the primary and functional traits, unfavorable impact of HS from the dry period on time-lagged performances in offspring was identified, even on longevity. From a practical perspective, our data suggest to provide HS abatement to late gestation dams to avoid long-term adverse effects on the offspring.

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits.

BACKGROUND: Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. RESULTS: SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). CONCLUSIONS: Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

Are scurs in heterozygous polled (Pp) cattle a complex quantitative trait?

BACKGROUND: Breeding genetically hornless, i.e. polled, cattle provides an animal welfare-friendly and non-invasive alternative to the dehorning of calves. However, the molecular regulation of the development of horns in cattle is still poorly understood. Studying genetic characters such as polledness and scurs, can provide valuable insights into this process. Scurs are hornlike formations that occur occasionally in a wide variety of sizes and forms as an unexpected phenotype when breeding polled cattle. METHODS: We present a unique dataset of 885 Holstein-Friesian cattle with polled parentage. The horn phenotype was carefully examined, and the phenotypic heterogeneity of the trait is described. Using a direct gene test for polledness, the polled genotype of the animals was determined. Subsequently, the existence of a putative scurs locus was investigated using high-density genotype data of a selected subset of 232 animals and two mapping approaches: mixed linear model-based association analyses and combined linkage disequilibrium and linkage analysis. RESULTS: The results of an exploratory data analysis indicated that the expression of scurs depends on age at phenotyping, sex and polled genotype. Scurs were more prevalent in males than in females. Moreover, homozygous polled animals did not express any pronounced scurs and we found that the Friesian polled allele suppresses the development of scurs more efficiently than the Celtic polled allele. Combined linkage and linkage disequilibrium mapping revealed four genome-wide significant loci that affect the development of scurs, one on BTA5 and three on BTA12. Moreover, suggestive associations were detected on BTA16, 18 and 23. The mixed linear model-based association analysis supports the results of the combined linkage and linkage disequilibrium analysis. None of the mapping approaches provided convincing evidence for a monogenic inheritance of scurs. CONCLUSIONS: Our results contradict the initial and still broadly accepted model for the inheritance of horns and scurs. We hypothesise an oligogenetic model to explain the development of scurs and polledness.

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.

Genome-wide associations and functional gene analyses for endoparasite resistance in an endangered population of native German Black Pied cattle.

BACKGROUND: Gastrointestinal nematodes (GIN), liver flukes (Fasciola hepatica) and bovine lungworms (Dictyocaulus viviparus) are the most important parasitic agents in pastured dairy cattle. Endoparasite infections are associated with reduced milk production and detrimental impacts on female fertility, contributing to economic losses in affected farms. In quantitative-genetic studies, the heritabilities for GIN and F. hepatica were moderate, encouraging studies on genomic scales. Genome-wide association studies (GWAS) based on dense single nucleotide polymorphism (SNP) marker panels allow exploration of the underlying genomic architecture of complex disease traits. The current GWAS combined the identification of potential candidate genes with pathway analyses to obtain deeper insights into bovine immune response and the mechanisms of resistance against endoparasite infections. RESULTS: A 2-step approach was applied to infer genome-wide associations in an endangered dual-purpose cattle subpopulation [Deutsches Schwarzbuntes Niederungsrind (DSN)] with a limited number of phenotypic records. First, endoparasite traits from a population of 1166 Black and White dairy cows [including Holstein Friesian (HF) and DSN] naturally infected with GIN, F. hepatica and D. viviparus were precorrected for fixed effects using linear mixed models. Afterwards, the precorrected phenotypes were the dependent traits (rFEC-GIN, rFEC-FH, and rFLC-DV) in GWAS based on 423,654 SNPs from 148 DSN cows. We identified 44 SNPs above the genome-wide significance threshold (pBonf = 4.47 × 10- 7), and 145 associations surpassed the chromosome-wide significance threshold (range: 7.47 × 10- 6 on BTA 1 to 2.18 × 10- 5 on BTA 28). The associated SNPs identified were annotated to 23 candidate genes. The DAVID analysis inferred four pathways as being related to immune response mechanisms or involved in host-parasite interactions. SNP effect correlations considering specific chromosome segments indicate that breeding for resistance to GIN or F. hepatica as measured by fecal egg counts is genetically associated with a higher risk for udder infections. CONCLUSIONS: We detected a large number of loci with small to moderate effects for endoparasite resistance. The potential candidate genes regulating resistance identified were pathogen-specific. Genetic antagonistic associations between disease resistance and productivity were specific for specific chromosome segments. The 2-step approach was a valid methodological approach to infer genetic mechanisms in an endangered breed with a limited number of phenotypic records.