Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament

Runs of Homozygosity Islands in Autochthonous Spanish Cattle Breeds

BACKGROUND/OBJECTIVES

Understanding the genetic architecture of autochthonous European cattle breeds is important for developing effective conservation strategies and sustainable breeding programs. Spanish beef cattle, which trace their origins to ancient migrations from the Near East with later admixture from African populations, exhibit a rich genetic diversity shaped by environmental adaptation and selective breeding. Runs of Homozygosity (ROH) are extended stretches of identical genetic material inherited from both parents. They serve as indicators of inbreeding and selection signatures within populations. ROH islands, or regions of the genome where ROH segments are highly concentrated across individuals within a breed, indicate genomic regions under selective pressure.

METHODS

This study explores the distribution of ROH islands across seven Spanish beef cattle breeds (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Retinta, Pirenaica, and Rubia Gallega). By analyzing high-density SNP data, we characterized ROH patterns and identified genomic regions with high levels of homozygosity, which may indicate selection pressures or common ancestry.

RESULTS

Our findings revealed breed-specific ROH patterns as well as shared ROH islands, underscoring genetic relationships and differentiation among the breeds. Notably, Morucha displayed the highest number of ROH, while Asturiana de los Valles had the fewest. FROH values, which indicate genomic inbreeding, varied among the breeds, with Morucha and Retinta being associated with higher values. We identified 57 ROH islands, with shared regions among populations that suggest common ancestral selection pressures. Key genes within these regions, like MSTN, are associated with muscle growth, body weight, and fertility.

CONCLUSIONS

This study offers valuable insights for breeding strategies and conservation efforts, highlighting the genetic diversity and historical background of Spanish cattle breeds.

Novel pathways linked to the expression of temperament in Merino sheep: a genome-wide association study

Animal temperament refers to the inherent behavioural and emotional characteristics of an animal, influencing how it interacts with its environment. The selection of sheep for temperament can change the temperament traits of the selected line and improve the welfare and production (reproduction, growth, immunity) of those animals. To understand the genetics that underly variation in temperament in sheep, and how selection on temperament can affect other production traits, a genome-wide association study was carried out. Merino sheep from lines selected for traits of calm and nervous temperament, and a commercial population, on which the temperament traits had never been assessed, were used. Blood samples from the three populations were genotyped using an Illumina GGP Ovine 50 K Genotyping BeadChip. The calm and nervous populations in the selected lines presented as distinct genetic populations, and 2 729 of the 45 761 single nucleotide polymorphisms (SNPs) had significantly different proportions between the two lines. Of those 2 729 SNPs, 2 084 were also associated with temperament traits in the commercial population. A genomic annotation identified 81 candidate genes for temperament, nearly half of which are associated with disorders of social behaviour in humans. Five of those 81 candidate genes are related to production traits in sheep. Two genes were associated with personality disorders in humans and with production traits in sheep. We identified significant enrichment in genes involved in nervous system processes such as the regulation of systemic arterial blood pressure, ventricular myocyte action, multicellular organismal signalling, ion transmembrane transport, and calcium ion binding, suggesting that temperament is underpinned by variation in multiple biological systems. Our results contribute to understanding of the genetic basis of animal temperament which could be applied to the genetic evaluation of temperament in sheep and other farm animals.

Adipose gene expression profiles in Northern Finncattle, Mirandesa cattle, Yakutian cattle and commercial Holstein cattle

The drastic change in global climate has led to in-depth studies of the geneticresources of native cattle adapted to challenging environments. Native cattle breeds may harbor unique genetic mechanisms that have enabled them adapt to their given environmental conditions. Adipose tissues are key factors in the regulation of metabolism and energy balance and are crucial for the molecular switches needed to adapt to rapid environmental and nutritional changes. The transcriptome landscape of four adipose tissues was used in this study to investigate the differential gene expression profiles in three local breeds, Yakutian cattle (Sakha Republic), Northern Finncattle (Finland), Mirandesa cattle (Portugal) and commercial Holstein cattle. A total of 26 animals (12 cows, 14 bulls) yielded 81 samples of perirenal adipose tissue (n = 26), metacarpal adipose tissue (n = 26), tailhead adipose tissue (n = 26) and prescapular adipose tissue (n = 3). More than 17,000 genes were expressed in our dataset. Principal component analysis of the normalized expression profiles revealed a differential expression profile of the metacarpal adipose tissue. We found that the genes upregulated in the metacarpal adipose tissue of Yakutian cattle, such as NR4A3, TEKT3, and FGGY, were associated with energy metabolism and response to cold temperatures. In Mirandesa cattle, the upregulated genes in perirenal adipose tissue were related to immune response and inflammation (AVPR2, CCN1, and IL6), while in Northern Finncattle, the upregulated genes appeared to be involved in various physiological processes, including energy metabolism (IGFBP2). According to the sex-based comparisons, the most interesting result was the upregulation of the TPRG1 gene in three tissues of Yakutian cattle females, suggesting that adaptation is related to feed efficiency. The highest number of differentially expressed genes was found between Yakutian cattle and Holstein, several of which were associated with immunity in Yakutian cattle, indicating potential differences in disease resistance and immunity between the two breeds. This study highlights the vast difference in gene expression profiles in adipose tissues among breeds from different climatic environments, most likely highlighting selective pressure and the potential significance of the uniquely important regulatory functions of metacarpal adipose tissue.

Characterization of the Temperament and Reactivity of Nelore Cattle (Bos indicus) Associated with Behavior Scores during Corral Management in the Humid Tropics

The evaluation of the reactivity and distress of cattle during corral management, by means of subjective scores, aims at the standardization of behavioral indicators, through non-invasive methods, in addition to enabling the development of more appropriate management practices, thus promoting the comfort and well-being of these animals. Therefore, in this study, we aimed to characterize the temperament and distress of cattle managed in a corral using behavioral indicators during the rainiest period. For this, the experiment was conducted on a property located in the municipality of Mojuí dos Campos, during the rainiest quarter (February-April). Thus, 30 male cattle, not castrated, approximately 29 months of age, clinically healthy, and weighing 310 + 20 kg, were divided into three rearing systems: silvopastoral (SP), traditional (SS), and integrated (SI) systems. There were 10 animals per system. Physiological parameters were collected to evaluate rectal temperature (RT) and respiratory rate (RR), as well as body surface temperature (BST), through thermal windows (head and flank infrared temperature and rump infrared temperature). To evaluate temperament and reactivity, scores indicative of corral behavior were used, namely escape speed (ES), tension score (SS_1), tension score (SS_2), reactivity scale (RS), movement score (MS), and temperament scale (TS). The results showed that there was a thermal amplitude of 5.9 °C on average and 8.6 °C at maximum when comparing the structure of the corral and the trees. In addition, the comparisons between the production systems for the behavioral variables did not differ at the 5% significance level, except for ES, where the traditional system differed from the integrated system and the silvopastoral system, showing intermediate average values for both. In addition, there was a positive correlation between the variables RT and RR (r = 0.72; p < 0.01), RR and SS_2 (r = 0.38; p = 0.04), flank infrared temperature and MS (r = 0.47; p = 0.01), rump infrared temperature and RS (r = 0.37; p = 0.04), SS_1 and RS (r = 0.41; p = 0.02), SS_1 and SS_2 (r = 0.39; p = 0.03), RS and SS_2 (r = 0.58; p = 0.00), RS and MS (r = 0.50; p = 0.01), RS and TS (r = 0.61; p = 0.00), SS_2 and MS (r = 0.51; p = 0.00), SS_2 and TS (r = 0.47; p = 0.01), and MS and TS (r = 0.44; p = 0.02), and a negative correlation between ES and TS (r = -0.42; p = 0.02). The rainy season had a major influence on the evaluation of temperature and distress levels during handling in the corral, as evidenced by the association between physiological and behavioral parameters.

Associations between genetically determined dietary factors and risk of autism spectrum disorder: a Mendelian randomization study

Background

Existing studies confirm the importance of dietary factors in developing autism spectrum disorder (ASD) and disease progression. Still, these studies are primarily observational, and their causal relationship is unknown. Moreover, due to the extensive diversity of food types, the existing research remains somewhat limited in comprehensiveness. The inconsistency of the results of some studies is very disruptive to the clinic. This study infers a causal relationship between dietary factors on the risk of developing ASD from a genetic perspective, which may lead to significant low-cost benefits for children with ASD once the specificity of dietary factors interfering with ASD is confirmed.

Methods

We performed a two-sample Mendelian randomization (MR) analysis by selecting single nucleotide polymorphisms (SNPs) for 18 common dietary factors from the genome-wide association study (GWAS) database as instrumental variables (IVs) and obtaining pooled data for ASD (Sample size = 46,351) from the iPSYCH-PGC institution. Inverse variance weighted (IVW) was used as the primary analytical method to estimate causality, Cochran's Q test to assess heterogeneity, the Egger-intercept test to test for pleiotropy and sensitivity analysis to verify the reliability of causal association results.

Results

The MR analysis identified four dietary factors with potential causal relationships: poultry intake (fixed-effects IVW: OR = 0.245, 95% CI: 0.084-0.718, P < 0.05), beef intake (fixed-effects IVW: OR = 0.380, 95% CI: 0.165-0.874, P < 0.05), cheese intake (random-effects IVW: OR = 1.526, 95% CI: 1.003-2.321, P < 0.05), and dried fruit intake (fixed-effects IVW: OR = 2.167, 95% CI: 1.342-3.501, P < 0.05). There was no causal relationship between the remaining 14 dietary factors and ASD (P > 0.05).

Conclusion

This study revealed potential causal relationships between poultry intake, beef intake, cheese intake, dried fruit intake, and ASD. Poultry and beef intake were associated with a reduced risk of ASD, while cheese and dried fruit intake were associated with an increased risk. Other dietary factors included in this study were not associated with ASD.

Analysis of nonsynonymous SNPs in candidate genes that influence bovine temperament and evaluation of their effect in Brahman cattle

BACKGROUND

Temperament is an important production trait in cattle and multiple strategies had been developed to generate molecular markers to assist animal selection. As nonsynonymous single nucleotide polymorphisms are markers with the potential to affect gene functions, they could be useful to predict phenotypic effects. Genetic selection of less stress-responsive, temperamental animals is desirable from an economic and welfare point of view.

METHODS AND RESULTS

Two nonsynonymous single nucleotide polymorphisms identified in HTR1B and SLC18A2 candidate genes for temperament were analyzed in silico to determine their effects on protein structure. Those nsSNPs allowing changes in proteins were selected for a temperament association analysis in a Brahman population. Transversion effects on protein structure were evaluated in silico for each amino acid change model, revealing structural changes in the proteins of the HTR1B and SLC18A2 genes. The selected nsSNPs were genotyped in a Brahman population (n = 138), and their genotypic effects on three temperament traits were analyzed: exit velocity, pen score, and temperament score. Only the SNP rs209984404-HTR1B (C/A) showed a significant association (P = 0.0144) with pen score. The heterozygous genotype showed a pen score value 1.17 points lower than that of the homozygous CC genotype.

CONCLUSION

The results showed that in silico analysis could direct the selection of nsSNPs with the potential to change the protein. Non-synonymous single nucleotide polymorphisms causing structural changes and reduced protein stability were identified. Only rs209984404-HTR1B shows that the allele affecting protein stability was associated with the genotype linked to docility in cattle.

Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats

The cross-species characterization of evolutionary changes in the functional genome can facilitate the translation of genetic findings across species and the interpretation of the evolutionary basis underlying complex phenotypes. Yet, this has not been fully explored between cattle, sheep, goats, and other mammals. Here, we systematically characterized the evolutionary dynamics of DNA methylation and gene expression in 3 somatic tissues (i.e. brain, liver, and skeletal muscle) and sperm across 7 mammalian species, including 3 ruminant livestock species (cattle, sheep, and goats), humans, pigs, mice, and dogs, by generating and integrating 160 DNA methylation and transcriptomic data sets. We demonstrate dynamic changes of DNA hypomethylated regions and hypermethylated regions in tissue-type manner across cattle, sheep, and goats. Specifically, based on the phylo-epigenetic model of DNA methylome, we identified a total of 25,074 hypomethylated region extension events specific to cattle, which participated in rewiring tissue-specific regulatory network. Furthermore, by integrating genome-wide association studies of 50 cattle traits, we provided novel insights into the genetic and evolutionary basis of complex phenotypes in cattle. Overall, our study provides a valuable resource for exploring the evolutionary dynamics of the functional genome and highlights the importance of cross-species characterization of multiomics data sets for the evolutionary interpretation of complex phenotypes in cattle livestock.

Effect of genotyping density on the detection of runs of homozygosity and heterozygosity in cattle

Runs of homozygosity (ROHom) are contiguous stretches of homozygous regions of the genome. In contrast, runs of heterozygosity (ROHet) are heterozygosity-rich regions. The detection of these two types of genomic regions (ROHom and ROHet) is influenced by the parameters involved in their identification and the number of available single-nucleotide polymorphisms (SNPs). The present study aimed to test the effect of chip density in detecting ROHom and ROHet in the Italian Simmental cattle breed. A sample of 897 animals were genotyped at low density (50k SNP; 397 individuals), medium density (140k SNP; 348 individuals), or high density (800k SNP; 152 individuals). The number of ROHom and ROHet per animal (nROHom and nROHet, respectively) and their average length were calculated. ROHom or ROHet shared by more than one animal and the number of times a particular SNP was inside a run were also computed (SNPROHom and SNPROHet). As the chip density increased, the nROHom increased, whereas their average length decreased. In contrast, the nROHet decreased and the average length increased as the chip density increased. The most repeated ROHom harbored no genes, whereas in the most repeated ROHet four genes (SNRPN, SNURF, UBE3A, and ATP10A) previously associated with reproductive traits were found. Across the 3 datasets, 31 SNP, located on Bos taurus autosome (BTA) 6, and 37 SNP (located on BTA21) exceeded the 99th percentile in the distribution of the SNPROHom and SNPROHet, respectively. The genomic region on BTA6 mapped the SLIT2, PACRGL, and KCNIP4 genes, whereas 19 and 18 genes were mapped on BTA16 and BTA21, respectively. Interestingly, most of genes found through the ROHet analysis were previously reported to be related to health, reproduction, and fitness traits. The results of the present study confirm that the detection of ROHom is more reliable when the chip density increases, whereas the ROHet trend seems to be the opposite. Genes and quantitative trait loci (QTL) mapped in the highlighted regions confirm that ROHet can be due to balancing selection, thus related to fitness traits, health, and reproduction, whereas ROHom are mainly involved in production traits. The results of the present study strengthened the usefulness of these parameters in analyzing the genomes of livestock and their biological meaning.

Unraveling the phenotypic and genomic background of behavioral plasticity and temperament in North American Angus cattle

BACKGROUND

Longitudinal records of temperament can be used for assessing behavioral plasticity, such as aptness to learn, memorize, or change behavioral responses based on affective state. In this study, we evaluated the phenotypic and genomic background of North American Angus cow temperament measured throughout their lifetime around the weaning season, including the development of a new indicator trait termed docility-based learning and behavioral plasticity. The analyses included 273,695 and 153,898 records for yearling (YT) and cow at weaning (CT) temperament, respectively, 723,248 animals in the pedigree, and 8784 genotyped animals. Both YT and CT were measured when the animal was loading into/exiting the chute. Moreover, CT was measured around the time in which the cow was separated from her calf. A random regression model fitting a first-order Legendre orthogonal polynomial was used to model the covariance structure of temperament and to assess the learning and behavioral plasticity (i.e., slope of the regression) of individual cows. This study provides, for the first time, a longitudinal perspective of the genetic and genomic mechanisms underlying temperament, learning, and behavioral plasticity in beef cattle.

RESULTS

CT measured across years is heritable (0.38-0.53). Positive and strong genetic correlations (0.91-1.00) were observed among all CT age-group pairs and between CT and YT (0.84). Over 90% of the candidate genes identified overlapped among CT age-groups and the estimated effect of genomic markers located within important candidate genes changed over time. A small but significant genetic component was observed for learning and behavioral plasticity (heritability = 0.02 ± 0.002). Various candidate genes were identified, revealing the polygenic nature of the traits evaluated. The pathways and candidate genes identified are associated with steroid and glucocorticoid hormones, development delay, cognitive development, and behavioral changes in cattle and other species.

CONCLUSIONS

Cow temperament is highly heritable and repeatable. The changes in temperament can be genetically improved by selecting animals with favorable learning and behavioral plasticity (i.e., habituation). Furthermore, the environment explains a large part of the variation in learning and behavioral plasticity, leading to opportunities to also improve the overall temperament by refining management practices. Moreover, behavioral plasticity offers opportunities to improve the long-term animal and handler welfare through habituation.

Genetic parameters for behavioral and growth traits of Nellore cattle

The growing concern of consumers with the welfare of production animals searches welfare in a production system extremely important; thus, the study of animal temperament is necessary to select less excitable temperament animals resulting in healthy development and fewer accidents. The objective of this study was to estimate genetic parameters for traits related to animal temperament and growth traits of Nellore cattle. In addition to exploring the genetic pattern of these traits through cluster and principal component analysis (PCA), to reveal possible groups of individuals that express less excitable temperament and greater growth. A total of 2,332 measurements from 1,245 male and female Nellore cattle born between 2008 and 2016 were utilized in the study. The (co)variance components were estimated by Bayesian inference using a two-trait animal model. The heritability for temperament score (TS), flight speed (FS), body condition score (BCS), live weight (LW), and hip height (HH) were 0.08, 0.12, 0.06, 0.13, and 0.48, respectively. The genetic correlation between the temperament indicator traits was strong and positive (0.78 ± 0.24). The TS and FS showed a favorable or null genetic correlation with LW, BCS, and HH. The third cluster included animals with low EBV for TS and FS and with high EBV for BCS, LW, and HH. In the PCA, the PC1 was what best evidenced the aim of this study; thus, our findings suggest that we could explore select animals based on cluster 3 and PC1 in breeding programs to select Nellore cattle with less excitable temperament and greater growth.

Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China

In aiming to achieve sustainable development goals in the livestock industry, it is becoming increasingly necessary and important for the effective conservation of genetic resources. There are some indigenous cattle breeds in Sichuan, southwest China, for which, however, the genetic diversity and population structures still remain unknown because of the unavailability of systematic breeding programs and pedigree information. Xieka cattle are an indigenous breed locally distributed in southeastern Sichuan and have a long-term evolutionary adaptation to local environments and climates. In this study, we obtained 796,828 single nucleotide polymorphisms (SNPs) through sequencing the genomes of 30 Xieka cattle and used them for analyzing the genetic diversity and runs of homozygosity (ROH). The mean nucleotide diversity was 0.28 and 72% of SNPs were found to be in the heterozygous states. A total of 4377 ROH were detected with even distribution among all autosomes, and 74% of them were lower than 1 Mb in length. Meanwhile, only five ROH were found longer than 5 Mb. We further determined 19 significant genomic regions that were obviously enriched by ROH, in which 35 positional candidate genes were found. Some of these genes have been previously reported to be significantly associated with various production traits in cattle, such as meat quality, carcass performances, and diseases. In conclusion, the relatively high degree of genetic diversity of Xieka cattle was revealed using the genomic information, and the proposed candidate genes will help us optimize the breeding programs regarding this indigenous breed.

Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits

Cattle temperament has been considered by farmers as a key breeding goal due to its relevance for cattlemen's safety, animal welfare, resilience, and longevity and its association with many economically important traits (e.g., production and meat quality). The definition of proper statistical models, accurate variance component estimates, and knowledge on the genetic background of the indicator trait evaluated are of great importance for accurately predicting the genetic merit of breeding animals. Therefore, 266,029 American Angus cattle with yearling temperament records (1-6 score) were used to evaluate statistical models and estimate variance components; investigate the association of sex and farm management with temperament; assess the weighted correlation of estimated breeding values for temperament and productive, reproductive efficiency and resilience traits; and perform a weighted single-step genome-wide association analysis using 69,559 animals genotyped for 54,609 single-nucleotide polymorphisms. Sex and extrinsic factors were significantly associated with temperament, including conception type, age of dam, birth season, and additional animal-human interactions. Similar results were observed among models including only the direct additive genetic effect and when adding other maternal effects. Estimated heritability of temperament was equal to 0.39 on the liability scale. Favorable genetic correlations were observed between temperament and other relevant traits, including growth, feed efficiency, meat quality, and reproductive traits. The highest approximated genetic correlations were observed between temperament and growth traits (weaning weight, 0.28; yearling weight, 0.28). Altogether, we identified 11 genomic regions, located across nine chromosomes including BTAX, explaining 3.33% of the total additive genetic variance. The candidate genes identified were enriched in pathways related to vision, which could be associated with reception of stimulus and/or cognitive abilities. This study encompasses large and diverse phenotypic, genomic, and pedigree datasets of US Angus cattle. Yearling temperament is a highly heritable and polygenic trait that can be improved through genetic selection. Direct selection for temperament is not expected to result in unfavorable responses on other relevant traits due to the favorable or low genetic correlations observed. In summary, this study contributes to a better understanding of the impact of maternal effects, extrinsic factors, and various genomic regions associated with yearling temperament in North American Angus cattle.

Haplotype-Based Single-Step GWAS for Yearling Temperament in American Angus Cattle

Behavior is a complex trait and, therefore, understanding its genetic architecture is paramount for the development of effective breeding strategies. The objective of this study was to perform traditional and weighted single-step genome-wide association studies (ssGWAS and WssGWAS, respectively) for yearling temperament (YT) in North American Angus cattle using haplotypes. Approximately 266 K YT records and 70 K animals genotyped using a 50 K single nucleotide polymorphisms (SNP) panel were used. Linkage disequilibrium thresholds (LD) of 0.15, 0.50, and 0.80 were used to create the haploblocks, and the inclusion of non-LD-clustered SNPs (NCSNP) with the haplotypes in the genomic models was also evaluated. WssGWAS did not perform better than ssGWAS. Cattle YT was found to be a highly polygenic trait, with genes and quantitative trait loci (QTL) broadly distributed across the whole genome. Association studies using LD-based haplotypes should include NCSNPs and different LD thresholds to increase the likelihood of finding the relevant genomic regions affecting the trait of interest. The main candidate genes identified, i.e., ATXN10, ADAM10, VAX2, ATP6V1B1, CRISPLD1, CAPRIN1, FA2H, SPEF2, PLXNA1, and CACNA2D3, are involved in important biological processes and metabolic pathways related to behavioral traits, social interactions, and aggressiveness in cattle. Future studies should further investigate the role of these candidate genes.

Adrenergic Tone as an Intermediary in the Temperament Syndrome Associated With Flight Speed in Beef Cattle

The temperament of farm animals can influence their resilience to everyday variations within the managed production environment and has been under strong direct and indirect selection during the course of domestication. A prominent objective measure used for assessing temperament in beef cattle is the behavioral flight response to release from confinement in a crush or chute. This behavioral measure, termed flight speed (also known as escape velocity) is associated with physiological processes including body temperature, feeding behavior, growth rate, carcass composition, immune function, and health outcomes. This review examines the functional links between this suite of traits and adrenergic activity of the sympathetic nervous system and the adrenomedullary hormonal system. It is suggested that flight speed is the behavioral aspect of an underlying “flightiness” temperament syndrome, and that elevated adrenergic tone in animals with a high level of flightiness (i.e., flighty animals) tunes physiological activities toward a sustained “fight or flight” defense profile that reduces productivity and the capacity to flourish within the production environment. Nonetheless, despite a common influence of adrenergic tone on this suite of traits, variation in each trait is also influenced by other regulatory pathways and by the capacity of tissues to respond to a range of modulators in addition to adrenergic stimuli. It is suggested that tuning by adrenergic tone is an example of homeorhetic regulation that can help account for the persistent expression of behavioral and somatic traits associated with the flight speed temperament syndrome across the life of the animal. At a population level, temperament may modulate ecological fit within and across generations in the face of environmental variability and change. Associations of flight speed with the psychological affective state of the animal, and implications for welfare are also considered. The review will help advance understanding of the developmental biology and physiological regulation of temperament syndromes.