Since 2014, abnormal mussel mortality (AMM) outbreaks have occurred along the French Atlantic coasts and mortality rates differed among years and sites (30–100%). Still, the etiology of the AMM is ...undefined. Our study explores the resistance of two mussel species (Mytilus edulis and Mytilus galloprovincialis) and natural hybrids (NH) cultivated in France to AMM. One hundred mussel families were produced using six wild mussel populations in January/February 2017. Mussels were tested in two sites, La Floride (LF) and Maison Blanche (MB), in October 2017, and their mortality/growth was recorded until June 2018. AMM was observed at MB during spring 2018, and reached 70%, 43%, and 63%, for M. edulis, M. galloprovincialis, and NH, respectively, at endpoint. In contrast, mortality was low in LF, reaching 11%, 30%, and 22%, respectively. Heritability for mortality was low to moderate in both sites ranging from 0.12 to 0.37 with higher values in M. edulis, intermediate for NH, and the lowest for M. galloprovincialis. A significant genotype-by-environment interaction was found for mortality between sites, with low genetic correlations not significantantly different from zero (−0.05 to 0.43). In July 2018, mussel families were evaluated under experimental infection using a pathogenic strain of Vibrio splendidus isolated during AMM in 2014. The mean mortality after 72 h post-injection was 53%, 22%, and 31% for M. edulis, M. galloprovincialis, and NH, respectively. The lowest heritability estimates were obtained for NH (0.21) and the highest for M. galloprovincialis (0.41), and the genetic correlation between AMM in MB and experimental infection was not significantly different from 0, suggesting that this Vibrio strain, is not the major cause of AMM outbreak observed in MB in 2018. Finally, significant genetic variation was observed for growth traits with mostly high heritability (> 0.44) for both species. Interestingly, genetic correlation between mortality and growth was weak and non-significant from zero.
•M. edulis is more susceptible to AMM than M. galloprovincialis.•Low to moderate heritability for resistance to AMM for both mussel species.•V. splendidus strain is not a major pathogen in AMM outbreaks in France in 2018•Significant G × E between sites.
Background
Observational and
in-vivo
research suggested a bidirectional relationship between depression and periodontitis. We estimated the genetic correlation and examined directionality of ...causation.
Methods
The study used summary statistics from published genome wide association studies, with sample sizes ranging from 45,563 to 797,563 individuals of European ancestry. We performed linkage disequilibrium score regression (LDSC) to estimate global correlation and used Heritability Estimation from Summary Statistics (ρ-HESS) to further examine local genetic correlation. Latent Heritable Confounder Mendelian randomization (LHC-MR), Causal Analysis using Summary Effect estimates (CAUSE), and conventional MR approaches assessed bidirectional causation.
Results
LDSC observed only weak genetic correlation (r
g
= 0.06, P-Value = 0.619) between depression and periodontitis. Analysis of local genetic correlation using ρ-HESS did not reveal loci of significant local genetic covariance. LHC-MR, CAUSE and conventional MR models provided no support for bidirectional causation between depression and periodontitis, with odds ratios ranging from 1.00 to 1.06 in either direction.
Conclusions
Results do not support shared heritability or a causal connection between depression and periodontitis.
Udder conformation is directly related to milk yield, cow health, workability, and welfare. Automatic milking systems (AMS, also known as milking robots) have become popular worldwide, and the number ...of dairy farms adopting these systems have increased considerably over the past years. In each milking visit, AMS record the location of the 4 teats as Cartesian coordinates in a xyz plan, which can then be used to derive udder conformation traits. AMS generate a large amount of per milking visit data for individual cows, which contribute to an accurate assessment of important traits such as udder conformation without the addition of human classifier errors (in subjective scoring systems). Therefore, the primary objectives of this study were to estimate genomic-based genetic parameters for udder conformation traits derived from AMS records in North American Holstein cattle and to assess the genetic correlation between the derived traits for evaluating the feasibility of multi-trait genomic selection for breeding cows that are more suitable for milking in AMS. The Cartesian teat coordinates measured during each milking visit were collected by 36 milking robots in 4,480 Holstein cows from 2017 to 2021, resulting in 5,317,488 records. A total of 4,118 of these Holstein cows were also genotyped for 57,600 single nucleotide polymorphisms. Five udder conformation traits were derived: udder balance (UB, mm), udder depth (UD, mm), front teat distance (FTD, mm), rear teat distance (RTD, mm), and distance front-rear (DFR, mm). In addition, 2 traits directly related to cow productivity in the system were added to the study: daily milk yield (DY) and milk electroconductivity (EC; as an indicator of mastitis). Variance components and genetic parameters for UB, UD, FTD, RTD, DFR, DY, and EC were estimated based on repeatability animal models. The estimates of heritability (±standard error, SE) for UB, UD, FTD, RTD, DFR, DY, and EC were 0.41 ± 0.02, 0.79 ± 0.01, 0.53 ± 0.02, 0.40 ± 0.02, 0.65 ± 0.02, 0.20 ± 0.02, and 0.46 ± 0.02, respectively. The repeatability estimates (±SE) for UB, UD, FTD, RTD, and DFR were 0.82 ± 0.01, 0.93 ± 0.01, 0.87 ± 0.01, 0.83 ± 0.01, and 0.88 ± 0.01, respectively. The strongest genetic correlations were observed between the FTD and RTD (0.54 ± 0.03), UD and DFR (−0.47 ± 0.03), DFR and FTD (0.32 ± 0.03), and UD and FTD (−0.31 ± 0.03). These results suggest that udder conformation traits derived from Cartesian coordinates from AMS are moderately to highly heritable. Furthermore, the moderate genetic correlations between these traits should be considered when developing selection sub-indexes. The most relevant genetic correlations between traits related to cow milk productivity and udder conformation traits were between UD and EC (−0.25 ± 0.03) and between DFR and DY (0.30 ± 0.04), in which both genetic correlations are favorable. These findings will contribute to the design of genomic selection schemes for improving udder conformation in North American Holstein cattle, especially in precision dairy farms.
At the beginning of lactation, high-producing cows commonly experience an unbalanced energy status that is often responsible for the onset of metabolic disorders and impaired health and performance. ...Blood β-hydroxybutyrate (BHB) and nonesterified fatty acids (NEFA) are indicators of excessive fat mobilization and circulating ketone bodies. Recently, prediction models based on mid-infrared (MIR) spectroscopy have been developed to assess blood BHB and NEFA from routinely collected individual milk samples. This study aimed to estimate genetic parameters of blood BHB and NEFA predicted from milk MIR spectra and to assess their phenotypic and genetic correlations with milk production and composition traits in early-lactation Holstein cows. The data set comprised the first test-day record within lactation and spectra of individual milk samples (n = 22,718) of 13,106 Holstein cows collected from 5 to 35 d in milk (DIM). Blood BHB and NEFA were predicted from milk MIR spectra using previously developed prediction models. Genetic parameters of blood metabolites and milk traits were estimated for the whole observational period (5–35 DIM) and within 6 classes of DIM. Blood BHB and NEFA showed similar genetic variation across DIM, with the highest heritability in the first 10 d after calving (0.31 ± 0.06 and 0.19 ± 0.05 for BHB and NEFA, respectively). The genetic correlation between BHB and NEFA was moderate (0.51 ± 0.05). Genetic correlations of BHB with milk yield, SCS, protein percentage, lactose percentage, and urea nitrogen content were similar to, or at least in the same direction as, the correlations of NEFA with the same traits, whereas opposite correlations were observed with fat percentage and fat-to-protein ratio. Results of the current study suggest that blood BHB and NEFA predicted from milk MIR spectra have genetic variation that is potentially exploitable for breeding purposes. Therefore, they could be used as indicator traits of hyperketonemia in a selection index aimed to reduce the susceptibility of dairy cows to metabolic disorders in early lactation.
•Sexual dimorphism is observed in genetic parameters and environmental sensitivity.•The inclusion of sex in defining the environmental descriptor introduces bias.•However, sex-specific analysis is ...appropriate for estimating genetic parameters.
This study investigates the environmental sensitivity and sexual dimorphism in the genetic parameters of weaning weight (WW) in Nelore beef cattle. Five reaction norms models were employed to analyze the 148,131 WW records, considering different definitions of the environmental descriptor (ED). (Co)variance components and genetic parameters were separately estimated for males and females. Results reveal substantial sexual dimorphism in various parameters. Significant divergence across sexes was observed for environmental sensitivity, with males showing an increased response to favorable environments while females genetically responded better to more challenging environments. Including sex in defining the ED can inflate the estimated breeding values of sires with a higher number of male progeny records, highlighting the importance of choosing a reliable ED in analyses of traits influenced by sexual dimorphism and genotype-by-environment interaction (G × E). The observed sexual dimorphism and environmental sensitivity underscore the complexity of genetic evaluation of WW in beef cattle populations, with implications for selection strategies. The findings suggest that a sex-separated trait analysis considering G × E effects is most appropriate for genetic evaluations of WW. However, a simpler single-trait model excluding sex from the ED definition yielded a higher coincidence of selected sires with the sex-separated analysis. In conclusion, understanding sexual dimorphism and environmental sensitivity is crucial for genetic evaluations and selection decisions in beef cattle breeding programs, emphasizing the need for careful model selection and ED definition.
•Mesenteric torsion (MT) is one of the major causes of sudden death in pigs.•The frequency of MT in the studied herd was 2.46 %, over 12 years of evaluation.•The pedigree and genomic heritabilities ...for MT were of low magnitude.•Selection to enhance feed conversion may reduce the occurrence of MT.•Lowering the 110 kg target age could decrease the occurrence of MT.
Mesenteric torsion (MT) is a condition characterized by the twisting of intestinal loops, leading to a disruption in blood flow and abdominal distension. Several factors can predispose animals to this condition, which primarily affects healthy, fast-growing pigs and often results in fatal outcomes. Given the absence of studies on the genetic factors associated with this condition, our research aimed to estimate the heritability coefficient for MT and explore the genetic correlations between MT and performance traits in pigs. Our dataset comprised of 43,384 records of pigs from a maternal line from a nucleus farm. These pigs were born between 2010 and 2022 and had recorded information regarding MT status (0 for healthy and 1 for affected animals), weaning weight (WW), as well as pedigree, genotypes, and genomic estimated breeding values (GEBVs) for the following traits: MT status, days to reach 110 kg (D110), feed conversion adjusted to 110 kg (FC110), and backfat thickness adjusted to 110 kg (BT110). In our statistical model, the effects of contemporary group (CG: sex, year, and week of weaning) and the linear covariate WW were considered fixed effects, while the direct additive genetic effect was accounted as random. On average, pigs affected by MT had an age of 104.35 ± 37.75 days, and the condition had an overall herd frequency of 2.46 %. Mesenteric torsion occurred more frequently in female pigs raised in collective pens compared to non-castrated males raised in individual pens. Heritability estimates for MT, using both pedigree (0.13 ± 0.02) and genomic (0.12 ± 0.02) data, were of low magnitude. This suggests that while there is genetic variability associated with MT, a significant portion of this variation is due to environmental variance. The correlation between MT and BT110 GEBVs was of low magnitude (0.05). In contrast, the correlations between GEBVs for MT and both D110 and FC110 were moderate in magnitude (0.22 for both traits). This implies that pigs taking longer to reach 110 kg and those with poorer feed conversion are more likely to develop MT. There is genetic variability for mesenteric torsion in pigs. Selection aimed at improving feed conversion and reducing the age at which pigs reach 110 kg could lead to a decrease in the occurrence of MT within pig populations.
Genetic influences on psychiatric disorders transcend diagnostic boundaries, suggesting substantial pleiotropy of contributing loci. However, the nature and mechanisms of these pleiotropic effects ...remain unclear. We performed analyses of 232,964 cases and 494,162 controls from genome-wide studies of anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, and Tourette syndrome. Genetic correlation analyses revealed a meaningful structure within the eight disorders, identifying three groups of inter-related disorders. Meta-analysis across these eight disorders detected 109 loci associated with at least two psychiatric disorders, including 23 loci with pleiotropic effects on four or more disorders and 11 loci with antagonistic effects on multiple disorders. The pleiotropic loci are located within genes that show heightened expression in the brain throughout the lifespan, beginning prenatally in the second trimester, and play prominent roles in neurodevelopmental processes. These findings have important implications for psychiatric nosology, drug development, and risk prediction.
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•Three groups of highly genetically-related disorders among 8 psychiatric disorders•Identified 109 pleiotropic loci affecting more than one disorder•Pleiotropic genes show heightened expression beginning in 2nd prenatal trimester•Pleiotropic genes play prominent roles in neurodevelopmental processes
Genome-wide analyses of eight different psychiatric disorders reveals common loci and shared genetic structures underlying many of them.
•The study focuses on health and routinely collected traits in Holstein cattle.•The events of health problems and culling were investigated in Holstein cattle.•The heritability and genetic ...correlation of health traits were estimated.•The approximate genetic correlations were estimated between health and routinely collected traits.•The results are beneficial for disease−resistance breeding in Holstein cattle.
Health traits have high economic values in dairy cattle breeding, which can cause considerable financial loss through involuntary culling. In this study, fourteen health traits were analysed, including five composite health traits: reproductive disorders, udder health (UH), digestive disorders, metabolic disorders, locomotory diseases (LD), and nine independent health traits: gestation disorders and peripartum disorders, irregular estrus cycle and sterility, metritis (ME), mastitis (MA), abomasal displacement (AD), enteritis (EN), and ketosis, claw diseases (CD), laminitis complex. This study analysed variance components for health traits through both single and bivariate repeatability animal models. All health traits showed low heritability, ranging from 0.001 to 0.025. Most of the health traits in five categories showed negative genetic correlations, ranging from −0.012 (CD and EN) to −0.634 (ME and EN). Strong positive genetic correlations appeared within the same category, ranging from 0.469 (EN and AD) to 0.994 (UH and MA, LD and CD). Furthermore, approximate genetic correlations were evaluated between health traits and routinely collected traits (longevity, fertility, production, and conformation). In general, the low to moderate approximate genetic correlations were estimated between health traits and routinely collected traits. The estimated correlations between health traits and longevity, fertility, production, and conformation traits could provide an indirect reference for disease−resistance breeding in Holstein cattle.
We present shaPRS, a method that leverages widespread pleiotropy between traits or shared genetic effects across ancestries, to improve the accuracy of polygenic scores. The method uses genome-wide ...summary statistics from two diseases or ancestries to improve the genetic effect estimate and standard error at SNPs where there is homogeneity of effect between the two datasets. When there is significant evidence of heterogeneity, the genetic effect from the disease or population closest to the target population is maintained. We show via simulation and a series of real-world examples that shaPRS substantially enhances the accuracy of polygenic risk scores (PRSs) for complex diseases and greatly improves PRS performance across ancestries. shaPRS is a PRS pre-processing method that is agnostic to the actual PRS generation method, and as a result, it can be integrated into existing PRS generation pipelines and continue to be applied as more performant PRS methods are developed over time.
We introduce shaPRS, a polygenic risk score (PRS) pre-processing method that improves predictive performance of PRSs by leveraging the genetic overlap between traits or ancestries. Importantly, shaPRS requires only GWAS summary statistics of two partially correlated traits or ancestries and is agnostic with respect to the method used to generate the PRSs.
Global genetic correlation analysis has provided valuable insight into the shared genetic basis between psychiatric and substance use disorders. However, little is known about which regions ...disproportionately contribute to the global correlation.
We used Local Analysis of coVariant Annotation to calculate bivariate local genetic correlations across 2495 approximately equal-sized, semi-independent genomic regions for 20 psychiatric and substance use phenotypes. We performed a transcriptome-wide association study using expression weights from the prefrontal cortex to identify risk genes for each phenotype, followed by probabilistic fine-mapping to prioritize credible causal genes within each bivariate locus.
We detected 80 significant (p < 2.08 × 10−6) bivariate local genetic correlations across 61 loci. The expression effect directions for risk genes within each bivariate locus were largely consistent with the local correlation coefficients, suggesting that genetically regulated gene expression may be used in the functional interpretation of local genetic correlations. Probabilistic fine-mapping identified several genes that may drive pleiotropic mechanisms for genetically correlated phenotypes. For example, we confirmed a local genetic correlation between schizophrenia and smoking behavior at 15q25 and prioritized PSMA4 as the most credible gene candidate underlying both phenotypes.
Our study reveals previously unreported local bivariate genetic correlations between psychiatric and substance use phenotypes, which we fine-mapped to identify shared credible causal genes underlying genetically correlated phenotypes.
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