A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders

Invited review: Phenotyping strategies and genetic background of dairy cattle behavior in intensive production systems-From trait definition to genomic selection

Understanding and assessing dairy cattle behavior is critical for developing sustainable breeding programs and management practices. The behavior of individual animals can provide valuable information on their health and welfare status, improve reproductive management, and predict efficiency traits such as feed efficiency and milking efficiency. Routine genetic evaluations of animal behavior traits can contribute to optimizing breeding and management strategies for dairy cattle but require the identification of traits that capture the most important biological processes involved in behavioral responses. These traits should be heritable, repeatable, and measured in noninvasive and cost-effective ways in many individuals from the breeding populations or related reference populations. Although behavior traits are heritable in dairy cattle populations, they are highly polygenic, with no known major genes influencing their phenotypic expression. Genetically selecting dairy cattle based on their behavior can be advantageous because of their relationship with other key traits such as animal health, welfare, and productive efficiency, as well as animal and handler safety. Trait definition and longitudinal data collection are still key challenges for breeding for behavioral responses in dairy cattle. However, the more recent developments and adoption of precision technologies in dairy farms provide avenues for more objective phenotyping and genetic selection of behavior traits. Furthermore, there is still a need to standardize phenotyping protocols for existing traits and develop guidelines for recording novel behavioral traits and integrating multiple data sources. This review gives an overview of the most common indicators of dairy cattle behavior, summarizes the main methods used for analyzing animal behavior in commercial settings, describes the genetic and genomic background of previously defined behavioral traits, and discusses strategies for breeding and improving behavior traits coupled with future opportunities for genetic selection for improved behavioral responses.

Exploration and Enrichment Analysis of the QTLome for Important Traits in Livestock Species

Background: Quantitative trait loci (QTL) are genomic regions that influence essential traits in livestock. Understanding QTL distribution and density across species' genomes is crucial for animal genetics research. Objectives: This study explored the QTLome of cattle, pigs, sheep, and chickens by analyzing QTL distribution and evaluating the correlation between QTL, gene density, and chromosome size with the aim to identify QTL-enriched genomic regions. Methods: Data from 211,715 QTL (1994-2021) were retrieved from the AnimalQTLdb and analyzed using R software v4.2.1. Unique QTL annotations were identified, and redundant or inconsistent data were removed. Statistical analyses included Pearson correlations and binomial, hypergeometric, and bootstrap-based enrichment tests. Results: QTL densities per Mbp were 10 for bovine, 4 for pig, 1 for sheep, and 3 for chicken genomes. Analysis of QTL distribution across chromosomes revealed uneven patterns, with certain regions enriched for QTL. Correlation analysis revealed a strong positive relationship between QTL and gene density/chromosome size across all species (p < 0.05). Enrichment analysis identified pleiotropic regions, where QTL affect multiple traits, often aligning with known candidate and major genes. Significant QTL-enriched windows (p < 0.05) were detected, with 699 (187), 355 (68), 50 (15), and 38 (17) genomic windows for cattle, pigs, sheep, and chickens, respectively, associated with overall traits (and specific phenotypic categories). Conclusions: This study provides critical insights into QTL distribution and its correlation with gene density, offering valuable data for advancing genetic research in livestock species. The identification of QTL-enriched regions also highlights key areas for future exploration in trait improvement programs.

Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan

Improving the low productivity levels of native cattle breeds in smallholder farming systems is a pressing concern in Pakistan. Crossbreeding high milk-yielding holstein friesian (HF) breed with the adaptability and heat tolerance of Sahiwal cattle has resulted in offspring that are well-suited to local conditions and exhibit improved milk yield. The exploration of how desirable traits in crossbred dairy cattle are selected has not yet been investigated. This study aims to provide the first overview of the selective pressures on the genome of crossbred dairy cattle in Pakistan. A total of eighty-one crossbred, thirty-two HF and twenty-four Sahiwal cattle were genotyped, and additional SNP genotype data for HF and Sahiwal were collected from a public database to equate the sample size in each group. Within-breed selection signatures in crossbreds were investigated using the integrated haplotype score. Crossbreds were also compared to each of their parental breeds to discover between-population signatures of selection using two approaches: cross-population extended haplotype homozygosity and fixation index. We identified several overlapping genes associated with production, immunity, and adaptation traits, including U6, TMEM41B, B4GALT7, 5S_rRNA, RBM27, POU4F3, NSD1, PRELID1, RGS14, SLC34A1, TMED9, B4GALT7, OR2AK3, OR2T16, OR2T60, OR2L3, and CTNNA1. Our results suggest that regions responsible for milk traits have generally experienced stronger selective pressure than others.

Genetic Foundations of Nellore Traits: A Gene Prioritization and Functional Analyses of Genome-Wide Association Study Results

The main goal of this study was to pinpoint functional candidate genes associated with multiple economically important traits in Nellore cattle. After quality control, 1830 genomic regions sourced from 52 scientific peer-reviewed publications were used in this study. From these, a total of 8569 positional candidate genes were annotated for reproduction, 11,195 for carcass, 5239 for growth, and 3483 for morphological traits, and used in an over-representation analysis. The significant genes (adjusted p-values < 0.05) identified in the over-representation analysis underwent prioritization analyses, and enrichment analysis of the prioritized over-represented candidate genes was performed. The prioritized candidate genes were GFRA4, RFWD3, SERTAD2, KIZ, REM2, and ANKRD34B for reproduction; RFWD3, TMEM120A, MIEF2, FOXRED2, DUSP29, CARHSP1, OBI1, JOSD1, NOP58, and LOXL1-AS1 for the carcass; ANKRD34B and JOSD1 for growth traits; and no genes were prioritized for morphological traits. The functional analysis pinpointed the following genes: KIZ (plays a crucial role in spindle organization, which is essential in forming a robust mitotic centrosome), DUSP29 (involved in muscle cell differentiation), and JOSD1 (involved in protein deubiquitination, thereby improving growth). The enrichment of the functional candidate genes identified in this study highlights that these genes play an important role in the expression of reproduction, carcass, and growth traits in Nellore cattle.

A Comprehensive Systematic Review Coupled with an Interacting Network Analysis Identified Candidate Genes and Biological Pathways Related to Bovine Temperament

Comprehension of the genetic basis of temperament has been improved by recent advances in the identification of genes and genetic variants. However, due to the complexity of the temperament traits, the elucidation of the genetic architecture of temperament is incomplete. A systematic review was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement to analyze candidate genes related to bovine temperament, using bovine as the population, SNPs and genes as the exposure, and temperament test as the outcome, as principal search terms for population, exposure, and outcome (PEO) categories to define the scope of the search. The search results allowed the selection of 36 articles after removing duplicates and filtering by relevance. One hundred-two candidate genes associated with temperament traits were identified. The genes were further analyzed to construct an interaction network using the STRING database, resulting in 113 nodes and 346 interactions and the identification of 31 new candidate genes for temperament. Notably, the main genes identified were SST and members of the Kelch family. The candidate genes displayed interactions with pathways associated with different functions such as AMPA receptors, hormones, neuronal maintenance, protein signaling, neuronal regulation, serotonin synthesis, splicing, and ubiquitination activities. These new findings demonstrate the complexity of interconnected biological processes that regulate behavior and stress response in mammals. This insight now enables our targeted analysis of these newly identified temperament candidate genes in bovines.

Identification of Candidate Genes and Pathways Linked to the Temperament Trait in Sheep

Temperament can be defined as the emotional variability among animals of the same species in response to the same stimulus, grouping animals by their reactivity as nervous, intermediate, or calm. Our goal was to identify genomic regions with the temperament phenotype measured by the Isolation Box Test (IBT) by single-step genome-wide association studies (ssGWAS). The database consisted of 4317 animals with temperament records, and 1697 genotyped animals with 38,268 effective Single Nucleotide Polymorphism (SNP) after quality control. We identified three genomic regions that explained the greatest percentage of the genetic variance, resulting in 25 SNP associated with candidate genes on chromosomes 6, 10, and 21. A total of nine candidate genes are reported for the temperament trait, which is: PYGM, SYVN1, CAPN1, FADS1, SYT7, GRID2, GPRIN3, EEF1A1 and FRY, linked to the energetic activity of the organism, synaptic transmission, meat tenderness, and calcium associated activities. This is the first study to identify these genetic variants associated with temperament in sheep, which could be used as molecular markers in future behavioral research.

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.

Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds

In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.

Genetic evaluation of crossbred Bos indicus cow temperament at parturition

Cow temperament at parturition may be mostly a measure of aggressiveness. The heritability of cow temperament at parturition in Bos taurus cows has been reported to be low. The objectives of this study were to estimate the heritability of cow temperament at parturition, conduct a genome-wide association analysis of cow temperament at the time of parturition, and estimate the correspondence of cow temperament at the time of parturition with cow productive performance and early-life temperament traits in Bos indicus crossbreds. Cow temperament was assessed from 1 to 5 indicating increasing levels of aggressiveness of cows (937 cows and 4,337 parturitions) from 2005 to 2022. Estimates of heritability and repeatability were 0.12 ± 0.024 and 0.24 ± 0.018. The estimates of proportion of phenotypic variance were 0.13 ± 0.019 and 0.02 ± 0.011 for permanent and maternal permanent environmental components, respectively. Estimates of heritability for maximum lifetime temperament score and proportions of temperament scores >1 were 0.18 ± 0.07 and 0.13 ± 0.072. Within cycles (generations), 2-yr-old cows had lower temperament score means than cows in most other age categories. There were low to moderate positive estimates of unadjusted correlation coefficients (r = 0.22 to 0.29; P < 0.05) of unadjusted temperament score with temperament measured on the same females when they were 8 mo old. There were low to moderate positive estimates of correlation coefficients (r = 0.09 to 0.37; P < 0.05) of unadjusted temperament score with calving rate, weaning rate, weaning weight per cow exposed, and weaning weight per 454 kg cow weight at weaning. Cows with the lowest temperament score had lower (P < 0.05) calving and weaning rate than cows in other temperament categories. Within 3 of 5 cycles, cows with the lowest temperament score (totally docile) had lower (P < 0.05) weaning weight per cow exposed than cows in other temperament categories. There were 2 SNP on BTA 4 associated with maximum lifetime temperament score (FDR < 0.05). The non-genetic influence of a cow's mother was documented in her own temperament measured at the time of calving; this may be a consequence of learned behavior. Less aggressiveness displayed by cows at the time of calving may be accompanied by lower reproductive and maternal performance.

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.

Behavioural Traits in Bos taurus Cattle, Their Heritability, Potential Genetic Markers, and Associations with Production Traits

People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a systematic review of literature pertaining to cattle genetics relating to behaviour. The review protocol was developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) framework, with Population, Exposure and Outcome components identified as Bovine, Genetics and Behaviour respectively. Forty-nine studies were identified in the sifting and assigned non-exclusively to groups of heritability (22), genomic associations (13) and production traits related to behaviour (24). Behavioural traits were clustered into the following groups: "temperament, disposition and/ or docility", "aggression", "chute score", "flight speed", "milking temperament", "non-restrained methods" and "restrained methods". Fourteen papers reported high accuracy (Standard Error ≤ 0.05) estimates of heritability, the majority (n = 12) of these studies measured over 1000 animals. The heritability estimates were found to vary between studies. Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible. These studies suggest that additive improvement of behavioural traits in cattle is possible and would not negatively impact performance. However, the variation between studies demonstrates that the genetic relationships are population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required.

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.

Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity

Natural adaptation and artificial selection have shaped the genome of modern livestock breeds. Among SNP-based metrics that are used to detect signatures of selection at genome-wide level, runs of homozygosity (ROH) are getting increasing popularity. In this paper, ROH distribution and features of a sample of 823 Sarda breed ewes farmed at different levels of altitude are analysed to investigate the effect of the environment on the patterns of homozygosity. A total of 46,829 (33,087 unique) ROH were detected. OAR2 exhibited the largest average number of ROH per animal. The most frequent ROH (OAR27, 38.9-44.2 Mb) was shared by 327. ROH length was statistically affected (p < 0.001) by both the altitude and temperature of the place where the flock was located. The highest probability of a SNP falling in a ROH was observed for hill ewes, whereas the smallest one for mountain. A total of 457 SNP exceeded the 99th percentile of the ROH count per SNP distribution and were considered significant. These markers mapped in eight chromosomes and they clustered into 17 ROH islands, where 80 candidate genes were mapped. Results of this study highlighted differences in the ROH distribution and features among sheep farmed in flocks located at different levels of altitude, confirming the role of environmental adaptability in shaping the genome of this breed.

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.