Traits In Animals Research Articles

Quantifying phenotypic variability of indigenous chickens using morphometric traits by applying multivariate analysis: Input for sustainable rural chicken farming

Despite environmentally influenced performance traits in farm animals, variations in morphometric characters reflect unswerving genetic effects. In this study, body weight and body dimension measurements of indigenous chickens reared in four rural communities were investigated using multivariate statistical procedures to elucidate the existence of phenotypic variability between chicken populations. The study districts were selected based on higher indigenous chicken population, geographic distance, and agro-ecological distinctiveness. Eleven morphometric traits were measured on 1060 adult chickens from the districts. The results revealed that there were significant (p < 0.0001) variations between populations across districts. Significantly (P < 0.0001) higher mean values for morphometric traits were obtained in chickens reared in the Hula (highland district) than in those of the three districts. Likewise, multivariate discriminant analysis showed that most of the variables had significant power to differentiate the chicken populations into separate groups. Accordingly, three discriminant functions were extracted, of which the first two explained 95.6 % of the total variances in the populations. Moreover, in cluster analysis, chickens were differentiated into two sub-groups: Hula as a separate population, and Shebedino, Aleta Chuko and Boricha populations clustered together. Furthermore, the discriminant analysis correctly assigned 56.7 %, 55.1 %, 51.5 %, and 53.3 % to their source populations of Hula, Aleta Chuko, Shebedino, Hula, and Boricha, respectively, showing high mixing and mobility of chickens across neighboring districts. Therefore, this study confirmed the existence of significant morphometric variability between the studied populations, which could be used as a valuable source of information for selective breeding and sustainable use of indigenous chickens, particularly for rural farmers who almost rely on phenotypic features to select breeding stocks. In addition, the higher morphometric measurements shown for Hula chickens should be confirmed by on-station evaluation, and further molecular tools should be applied to validate the genetic distinctiveness of the studied chicken populations.

Some Yield and Growth Traits of Anatolian Buffaloes and the Effects of First Calving Age and Calving Interval on These Traits

Numerous in-depth studies have described the fertility traits, growth performance and milk yield traits of dairy animals, which are considered indicators of welfare, but there are limited studies examining these traits within the framework of cause-effect relationships, especially in buffaloes. The aim of this study was to determine the changes in some milk, growth and fertility traits of Anatolian buffaloes over the years in some dairy farms where the Buffalo Breeding Project in Public Conditions was implemented in Samsun province and, to investigate the effects of first calving age (FCA) and calving interval (CI) on milk and growth traits. The study was conducted in 27 buffalo farms (3295 buffalo cows and 3317 buffalo calves) located in Bafra district, the region with the highest buffalo population in Samsun province, Türkiye. The data was taken from records previously kept within the scope of the relevant project. The data such as growth characteristics [birth weight (BW), 6th and 12th-mo live weight (LW) values of calves born between 2013-2020] and lactation traits of cows [lactation milk yield (LMY) and lactation duration (LD)] and FCA and CI values were analyzed by analysis of variance. The effect of years on LMY of buffalo cows was found to be significant, and significant positive changes were determined from year to year. In addition, the BW, 6th-mo, and 12th-mo LW values of calves also varied from year to year. As the FCA value of buffaloes increased, the BW, 6th-mo, and 12th-mo LW values of calves and LMY of cows increased. Similarly, CI values affected the BW values of calves (P&lt;0.01), and LMY and LD values increased in parallel with the increase in CI values. Consequently, determining the lactation and growth traits of buffaloes could benefit developing herd management practices that would optimize these performance indicators.

Effect of host breeds on gut microbiome and fecal metabolome in commercial pigs

BackgroundGut microbial composition and its metabolites are crucial for livestock production performance. Metabolite profiles from autopsied biospecimens provide vital information on the basic mechanisms that affect the overall health and production traits in livestock animals. However, the role of the host breed in the gut microbiome and fecal metabolome of commercial pigs remains unclear. In this work, differences in microbiota composition among three commercial pig breeds Duroc, Yorkshire, and Landrace were measured by 16S rRNA gene sequencing. Fecal metabolite compositions of the three pig breeds were detected using untargeted metabolomics.ResultsThere were significant differences in the gut microbiomes of the three species, indicating that host breed affects the diversity and structure of gut microbiota. Several breed-associated microorganisms were identified at different taxonomic levels. Notely, most microbial taxa were annotated as Lactobacillacea, Muribaculaceae, and Oscillospiraceae. Several bacteria, including Lactobacillus, Subdoligranulum, Faecalibacterium, Oscillospira, Oscillospiraceae_UCG-002, and Christensenellaceae_R-7_group, could be considered as biomarkers for improving the backfat thickness (BF) for commercial pigs. Additionally, KEGG analysis of gut microbiota further revealed that arginine biosynthesis, pyruvate metabolism, and fatty acid biosynthesis varied greatly among pig breeds. Multiple gut bacterial metabolites (e.g., spermidine, estradiol, and palmitic acid) were identified as breed-associated. Mediation analysis ultimately revealed the cross-talk among gut microbiota, metabolites, and BF thickness, proclaiming that the microbial and metabolic biomarkers identified in this study could be used as biomarkers for improving BF phenotype.ConclusionsThis work provides vital insights into breed effects on gut microbiota and metabolite compositions of commercial pigs and uncovers potential biomarkers that are significant for pig breed improvement.

Seasonally Changing Interactions of Species Traits of Termites and Trees Promote Complementarity in Coarse Wood Decomposition.

Complementary resource use by functionally different species may accelerate ecosystem processes. However, how co-variation in plant traits and animal traits promotes complementarity through temporal plant-animal interactions is poorly understood, even less so in detrital systems, thereby hampering our fundamental understanding of decomposition and carbon turnover. We hypothesised that, in seasonal subtropical forests where termites are major deadwood decomposers, trait complementarity of both termite species and tree species should promote overall deadwood decomposition through different seasons and years. Findings from a four-year coarse wood decomposition experiment involving 27 tree and 5 termite species support this hypothesis. Phenological and mandibular traits of the two most abundant termite species controlled wood decomposition of tree species differing in wood traits, through the seasons over 4 years, thereby promoting overall deadwood decomposition rates. Our findings indicate that complementarity in functional trait co-variation in plants and animals plays an important role in carbon cycling.

Genetic analysis of key agronomic traits of local sheep breeds in Xinjiang, China

The formation of sheep (Ovis aries) breeds is influenced by different ecological environments and populations with different living habits, resulting in the development of germplasm resources with stable genetic key agronomic traits. Thus, investigating the genetic mechanisms behind various agronomic traits can enhance the conservation and utilization of diverse sheep breeds. Here, we explored the sheep variome and selection signatures using the Ovine Infinium HD SNP BeadChip (600 K SNPs) from 23 sheep breeds, comprising a total of 1215 sheep. The genetic mechanisms of wool quality and tail morphology were analyzed by selective sweep and genome-wide association study. Based on the results of within-population selective sweep analysis, we performed gene network analysis and divided them into 6 gene communities. We identified genetic regions containing genes linked to sheep wool and tail, which have been and may continue to be important targets for breeding and selection. Furthermore, our results revealed the expression profiles of genes in these regions across different biological systems. Our study provides insights into categorizing sheep breeds into distinct gene communities, as well as references for constructing genetic network pathways related to key agronomic traits in sheep and other domestic animals.

The resistance of domestic canine skin-derived fibroblasts to oxidative and non-oxidative chemical injury: implications of breed and body size.

Small-breed dogs live significantly longer lives than large-breed dogs, while having higher mass-specific metabolic rates and faster growth rates. Underlying this observed physiological difference across domestic dogs, there must also be differences at other levels of organization that could lead to elucidating what accounts for the disparity in aging rates and life span within this species. At the cellular level, a clear mechanism underlying whole animal traits has not been fully elucidated. Here, we cultured dermal fibroblasts from large and small breed dogs from both young and old age categories and examined the degree of resistance to multiple sources of cytotoxic stress. This included heat (42°C), paraquat, cadmium, and hydrogen peroxide for increasing amounts of time (heat) or increasing concentrations (chemical stressors). We hypothesized that small breed dogs, with longer lifespans, would have greater cellular resistance to stress compared with large breed dogs. Final sample sizes include small puppies (N = 18), large puppy (N = 32), small old (N = 11), and large old (N = 23) dogs. Using a 2 (donor size) by 2 (donor age) between-subjects multivariate analysis of variance, we found that the values for the dose that killed 50% of the cells (LD50) were not significantly different based on donor size (p = 0.45) or donor age (p = 0.20). The interaction was also not significant (p = 0.47). Interestingly, we did find that the degree of resistance to cadmium toxicity was significantly correlated with the degree of resistance to both heat and hydrogen peroxide, but not paraquat (p < 0.01 for both). These data suggest that cellular stress resistance does not differ among domestic dogs as a function of size or age, pointing to other cellular pathways as the mechanistic basis for the observed differences in lifespan.

Bold rats (Niviventer confucianus) are more effective in seed dispersal: evidence both under enclosure conditions and in the field.

Rodents are important seed dispersers of plants because they move seeds far away from the parent trees and hoard seeds in the soil, benefiting seed dispersal and regeneration. Traits of plant seeds and animals are associated with rodent-mediated seed dispersal, but animal personality, the consistent individual behavioral differences in time and environments, has not been fully considered. Here, we first measured the personality of 26 Niviventer confucianus in the laboratory, and 10 individuals in the field of one population, and then tested their behavior of seed consumption and hoarding both in semi-natural enclosures and the field. We tested the hypothesis that individuals with different personalities have different preferences for seed consumption and hoarding, which has different implications for seed dispersal and regeneration. Under the enclosure conditions, all parameters of personality are repeatable; bold individuals harvested fewer seeds but scatter-hoarded more seeds and dispersed farther than timid ones, whereas active individuals consumed more seeds, but left fewer seeds on the ground surface than inactive ones. In the field, boldness, activity, and exploration of the animals are repeatable; bold individuals scatter-hoarded more seeds to farther distances than timid ones, whereas active individuals harvested and consumed more seeds than inactive ones. These results suggest that bold rats tended to scatter hoard seeds and disperse them to a longer distance, implying they are more effective in seed dispersal. In the future, animal personality (e.g. boldness and activity) should be considered in seed dispersal studies and ecological-based manipulation in seed dispersal and regeneration of forests.

Willingness to pay for sheep traits and their heterogeneous effects on prices: Evidence from primary livestock markets in Ethiopia

We test the hypothesis whether levels of key traits of sheep heterogeneously affect market prices of sheep in a rural setting. Feasible generalized least squares and (un)conditional quantile regression estimations were made on a dataset of 1153 sheep transactions in two primary small ruminant markets in the Amhara region of Ethiopia. The empirical results show that animal traits affect the observed prices of sheep differently, but only partly explain the sheep price differences. Our results also reveal that in addition to animal traits, the type of buyers and seasonality of sheep marketing cause heterogeneity in the observed prices. These findings imply that targeting the animal traits demanded by the market and access to price information that enables farmers to respond to the seasonal changes in livestock markets are essential to increase the income of sheep keepers.

Oxidative Challenges Do Not Impact Pheomelanin-Dependent Coloration in Male Japanese Quails.

Colorful traits play an important role in animal communication. Melanin-based colorations are the most extended color traits in animals and are produced by two types of endogenous melanic pigments: eumelanins and pheomelanins, the last ones being the least studied in the context of communication. The production of pheomelanin requires a semi-essential amino acid, cysteine, which is also used for the synthesis of an important endogenous antioxidant, glutathione. Hence, it has been proposed that the synthesis of pheomelanin and glutathione may compete for the cysteine available in the organism. In that case, pheomelanic colorations are predicted to be less intense when the individual is facing an oxidative challenge, and therefore, they would provide information on the oxidative status of the bearer. Here, we experimentally evaluated this hypothesis using male Japanese quails (Coturnix japonica) as a model of study, a species with pheomelanin-based plumage in the breast and cheeks. During feather growth, individuals were exposed to one of three possible conditions: Control (saline), an endogenous oxidative challenge (Escherichia coli lipopolysaccharide injections), or an exogenous oxidative challenge (paraquat injections). Contrary to predictions, we found that: (1) Birds from the three groups exhibited less intense pheomelanic colorations in feathers after the experimental manipulation, and the magnitude of this change did not differ among groups. (2) There was no effect of the experimental treatments on the proportion reduced/oxidized glutathione, an index of oxidative status. (3) Lipid peroxidation was lower after the experimental manipulation, with birds exposed to the paraquat challenge experiencing a stronger decline than other groups. (4) Cysteine and total glutathione levels decreased after the experimental manipulation, with no differences per group in the magnitude of the decline. Taken together the results do not support the hypothesis that oxidative status plays a key role at determining the variation in the intensity of pheomelanic colorations.

309 Synergistic optimization: Utilizing genomic insights to enhance strategies for joint selective (deep) phenotyping and recursive creation of genomic reference populations - Sponsored by EAAP

Abstract Synergistic optimization is a process combining different elements achieving better results than would be possible by optimizing each element individually. Our objective will be to design systems where genotyping and phenotyping complement each other to achieve superior performance. Deep phenotyping can be defined as a comprehensive and detailed approach to characterize traits of animals, including those based on the study of intermediate phenotypes representing not only the phenome, but also e.g., the metabolome, the proteome, and the transcriptome (i.e., -omics phenotypes). Often these phenotypes are also called high-throughput but this should not be considered being a synonym for being cheap. Interplay between genotyping and (deep) phenotyping has a major impact on the acquisition of genetic knowledge but could also be used in the context of genomic evaluations (i.e., as intermediate correlated features such as high-throughput or -omics phenotypes). While past studies have largely focused on ways to integrate deep phenotyping to gain new knowledge but also to support genetic and genomic evaluations, phenotyping and especially deep phenotyping currently requires massive investment, limiting its effective and widespread use under field, but also in experimental conditions. This problem extends to complex phenotype-taking as feed intake, methane emissions or in general use of expensive sensors. Even with all the possible investments, many phenotyping efforts are limited by the poor choice of animals. This presentation will address and introduce the topic of genome-enabled optimization of (deep) phenotyping taking into account the facts that genotypes are in many cases much cheaper than phenotyping, can be performed at early stages, and can help organize animal sampling in an efficient manner. The last point is also linked to validation techniques comparing predicted to observed phenotypes and closely related to recursive genomic reference population building issues. Techniques used in other fields such as chemometrics (i.e., infrared spectra prediction building) will be proposed to optimize covering genetic variability. In the context of recursively performed genomic evaluations (i.e., increasing reference population at each round) population accuracy and bias of prediction will be addressed. Moreover, long term genetic contribution and population structure issues will have to be considered. Based on literature and practical examples systematically organized sampling techniques will be presented to discuss basic principles as covering observed genomic and expected phenotypic diversity and long-term effects of recursively created genomic reference populations.

Turning up the heat: Effects of temperature on agonistic acoustic communication in the two-spotted goby (Pomatoschistus flavescens)

Acoustic communication is linked to fitness traits in many animals, but under the current scenario of global warming, sound signals can be affected by rising temperatures, particularly in ectothermic organisms such as fishes. This study examines the effect of water temperature in acoustic communication in the two-spotted goby, Pomatoschistus flavescens. To address this, we looked at the effect of different temperatures on the acoustic features of drums produced by males during territorial defence and related it with their auditory sensitivity. We also analysed the differences in acoustic features between male agonistic drums and previously reported male courtship sounds, to better understand how acoustic communication may be affected by different temperature conditions. We recorded two-spotted goby males during territorial intrusions for 10 min at 16 °C, 19 °C, and 21 °C in the laboratory. We found that agonistic drums were shorter, had fewer pulses and shorter pulse periods at higher temperature, in contrast with the peak frequency that remained unaffected. Male agonistic and mating drums (recorded in a previous study) at 16 °C only differed in pulse period, which was higher in mating drums. Hearing thresholds obtained with Auditory Evoked Potentials at 16 °C, revealed higher sensitivity below 400 Hz, matching the main energy of agonistic and mating sounds. Our findings suggest that increasing temperature could potentially affect acoustic communication in this species by reducing the duration of agonistic drums, which might hinder effective communication. Nevertheless, the impact may not be significant as there was a good match between the best hearing sensitivity and the peak frequency range of their calls, which was not influenced by temperature. As fish and other organisms are increasingly threatened by multiple anthropogenic stressors, including warming, future research should address how changes in water temperature impact acoustic communication within a more realistic multi-stressor scenario.

InDel mutations within the bovine PER2 gene are significantly associated with reproductive traits.

Functioning as a key regulator of circadian rhythms, the PER2 gene exerts a substantial impact on the reproductive traits of animals. However, the effect of the PER2 gene on ovarian development remains unclear. In order to examine the relationship between bovine reproductive trait and the PER2 gene, a total of 901 ovarian samples were collected, categorized into different oestrus cycles (proestrus, oestrus, post-oestrus, anoestrous), and subjected to analysis for two potential insertion/deletions (InDels) in the PER2 gene. Through agarose gel electrophoresis and DNA sequencing, two polymorphic deletion mutations (P2-D5-bp, P3-D13-bp) were identified. Furthermore, a significant association between mature follicle diameter and P2-D5-bp was found (P < 0.05). Additionally, several significant correlations with ovarian length, width, height, and white body diameter were found for P3-D13-bp (P < 0.05). These findings suggested that the bovine PER2 gene plays an important role in above-mentioned reproductive traits, offering new avenues for improving cow fertility through marker-assisted selection (MAS).

Commercial perspectives: Genome editing as a breeding tool for health and well-being in dairy cattle

Genome editing is the latest breeding tool capable of accelerating the rate of genetic improvement for health and well-being traits in food animals. It enables the introduction of beneficial alleles within a single generation, including those of low frequency or absent in the population, while effectively bypassing linkage drag. For the dairy industry, genome editing can be used to make rapid genetic improvements that are precise, efficient, and transgene-free for functional traits that are not practically addressed without disrupting conventional breeding goals for overall economic merit based on genomic selection. Herein, various case studies for dairy cattle breeding are presented that demonstrate applications of genome editing for enhancing heat stress tolerance, reduced disease susceptibility, and/or other qualitative traits absent in some breeds. One case highlights the success of simultaneous editing of multiple loci through recent advancements in embryonic stem cell biology. Multiplexed editing is crucial for addressing the polygenic nature inherent to many economically important traits in livestock. However, maximizing the benefits of genome editing depends on the continued discovery of targets for editing that are commercially important. Commercialization also depends on rapidly evolving regulatory statutes for risk assessment, where some countries already permit the commercialization of cattle with non-GMO genome alterations through existing regulations. New breeding technologies like genome editing are now poised to have significant impact in equipping elite performance cattle to be more resilient to infectious disease and climate change without the loss of production gains obtained from decades of selection.

The Impact of Horse-Assisted Therapy on Socio-Emotional Behaviors in Children with Autism

Animal-assisted therapy for children with autism (ASD) is a form of complementary therapy, integrating methods from various other types of therapy. AAT, or animal-assisted therapy, is a series of interventions that are based on the behavioral traits of animals, especially dogs and horses, which are the most common in this context. These interventions can be integrated into conventional treatments such as behavioral therapy, play therapy, music therapy, occupational therapy, speech therapy, and art therapy, depending on the individual needs of patients. The objective of this study was to examine the effects of an already existing Equine Assisted Therapy (EAT) program on social communication skills, executive functions and motor skills in children diagnosed with autism spectrum disorders. The research adopted an observational design to analyze how often certain behaviors occur in the presence or absence of horses in a group intervention program. This research included 16 children diagnosed with autism spectrum disorder (ASD), aged between 9 and 14 years (12 boys and 4 girls), who were selected from an School Center for Inclusive Education. The conclusions drawn from our results showed that the horse-assisted therapy, implemented in our experiment, recorded a notable improvement in all the behavioral parameters analyzed. Improvements were observed in Attention in Activity (21.2%), Communication (18.3%) and Compliance (9.1%) during activities, Physical Movements, with a difference of 34.1%, Affective State (23.33%), Visual Control (45%), Functional Skills and Response to Command (46.66%), Social Attention (33.5%) and Dynamic Motor Skills (35.55%) during activities. And the biggest difference was observed in Vocalizations, with a difference of 53%. Our results strongly support the fact that complementary therapy of autism spectrum disorders with the help of horses is an effective form of intervention, which can bring substantial improvements in therapeutic outcomes.

Microbial Community Structure and Metabolism of Xinjiang Fine-Wool Sheep based on High-Throughput Sequencing Technology.

It turns out that the more than trillion microorganisms living in the host's digestive tract are crucial for maintaining nutrient intake, environmental suitability, and physiological mechanism. Xinjiang fine-wool sheep is an exclusive breed for wool in China, which has excellent stress tolerance. In this study, we collected feces and blood samples of 20 Xinjiang fine-wool sheep under the same genetic characteristics, the Fine-Wool Sheep (FWS) group and the Control Fine-Wool Sheep (CFWS) group were set up according to the differs in phenotypic characteristics of their wool. By 16S rRNA amplicon sequence, ITS1 region amplicons and Targeted Metabolomics, we analyzed the microbial community structure of fecal microorganisms and Short Chain Fatty Acids (SCFAs) in serum of the Xinjiang fine-wool sheep. Fecal microbial sequencing showed that the bacterial composition and structure were similar between the two groups, whereas there were significant differences in the composition and structure of the fungal community. It was also found that the abundant of Neocallimastigomycota in the intestinal fungal community of FWS was higher. In addition, the results of the serum SCFAs content analysis showed that butyric acid was significantly differences than those two groups. Correlation analysis between SCFAs and bacteria found that butyric acid metabolism had positively correlated (P < 0.05) with Ruminococcus and UCG-005. Overall, our data provide more supplement about the gut microbes community composition and structure of the Xinjiang fine-wool sheep. These results might be useful for improving gut health of sheep and taking nutritional control measure to improve production traits of animals in future.

Application of GWAS and mGWAS in Livestock and Poultry Breeding.

In recent years, genome-wide association studies (GWAS) and metabolome genome-wide association studies (mGWAS) have emerged as crucial methods for investigating complex traits in animals and plants. These have played pivotal roles in research on livestock and poultry breeding, facilitating a deeper understanding of genetic diversity, the relationship between genes, and genetic bases in livestock and poultry. This article provides a review of the applications of GWAS and mGWAS in animal genetic breeding, aiming to offer reference and inspiration for relevant researchers, promote innovation in animal genetic improvement and breeding methods, and contribute to the sustainable development of animal husbandry.

Effects of GH L127V and TG5 C422T polymorphisms on the hormonal profile, slaughter traits, and meat quality of Hereford bulls.

The creation of objective methods for the evaluation and improvement of quantitative and qualitative indicators of meat productivity in farm animals should be based on a comprehensive analysis of the genetic, physiological, and biochemical parameters of the animal. This study aimed to investigate the effects of growth hormone (GH) and thyroglobulin (TG5) gene polymorphisms on the hormonal status, slaughter traits, and chemical, amino acid, and fatty acid composition of meat in Hereford bulls. Hereford bulls (n = 9) were reared under the same feeding and housing conditions until the age of 21 months, after which they were slaughtered. Polymerase chain reaction-restriction fragment length polymorphism was performed for genotyping GH L127V and TG5 C422T polymorphisms. The experimental animals were evaluated to determine slaughter traits (including pre-slaughter weight, carcass, and internal fat weight and yield), chemical, fatty acid, and amino acid composition of ground beef, and hormonal status using serum concentrations of GH, triiodothyronine, and thyroxine. Animals with the valine homozygous (VV) genotype of GH had the maximum serum GH level of 9.33 mIU/mL (p = 0.10) higher than leucine homozygous (LL) genotype carriers. Individuals with the LL genotype outperformed V-allele carriers in serum thyroxine (T4) concentration by 21.3-30.5 nmol/L (16.15%-24.86%; p < 0.01-0.05). Genetic differentiation induced by TG5 C422T polymorphism was determined to a lesser extent by the hormonal status of the Hereford animals. The V-allele was associated with increased carcass weight, with VV homozygotes significantly outperforming LL individuals by 45.0 kg (13.61%; p < 0.05). The T allele at the TG5 gene polymorphism was associated with more intense lipogenesis and less protein synthesis in muscle tissue and these effects were enhanced in the homozygous state. Young animals with the TT variant of the TG5 gene exhibited a significantly superior polyunsaturated fatty acid/saturated fatty acid ratio of 0.012 units (p < 0.01). Carriers of the LL genotype were characterized by minimum amino acid content in muscle tissue. Heterozygous bulls exceeded LL homozygotes in the sum of essential amino acids by 3.09% (p = 0.10) and non-essential amino acids by 1.9% (p < 0.05). The development of breeding programs for the Hereford breed should be carried out considering genetic features that determine the formation of economic traits in animals. Analysis of polymorphisms in the TG5 gene is a promising method for the early diagnosis of the fatty acid composition of beef. Identification of polymorphisms in the GH gene allows the prediction of higher productivity potential and amino acid composition of meat. The different effects of the GH and TG5 genes on the development of various economic traits allowed us to determine further vectors for scientific research on their complex associations in Hereford cattle, which will be useful for planning effective breeding schemes.

Ontologies related to livestock for the Global Burden of Animal Diseases programme: a review.

The Global Burden of Animal Diseases (GBADs) programme aims to assess the impact of animal health on agricultural animals, livestock production systems and associated communities worldwide. As part of the objectives of GBADs'Animal Health Ontology theme, the programme reviewed conceptual frameworks, ontologies and classification systems in biomedical science. The focus was on data requirements in animal health and the connections between animal health and human and environmental health. In May 2023, the team conducted searches of recognised repositories of biomedical ontologies, including BioPortal, Open Biological and Biomedical Ontology Foundry, and Ontology Lookup Service, to identify animal and livestock ontologies and those containing relevant concepts. Sixteen ontologies were found, covering topics such as surveillance, anatomy and genetics. Notable examples include the Animal Trait Ontology for Livestock, the Animal Health Surveillance Ontology, the National Center for Biotechnology Information Taxonomy and the Uberon Multi-Species Anatomy Ontology. However, some ontologies lacked class definitions for a significant portion of their classes. The review highlights the need for domain evidence to support proposed models, critical appraisal of external ontologies before reuse, and external expert reviews along with statistical tests of agreements. The findings from this review informed the structural framework, concepts and rationales of the animal health ontology for GBADs. This animal health ontology aims to increase the interoperability and transparency of GBADs data, thereby enabling estimates of the impacts of animal diseases on agriculture, livestock production systems and associated communities globally.

Variation and Interaction of Distinct Subgenomes Contribute to Growth Diversity in Intergeneric Hybrid Fish.

Intergeneric hybridization greatly reshapes regulatory interactions among allelic and non-allelic genes. However, their effects on growth diversity remain poorly understood in animals. In this study, we conducted whole-genome sequencing and RNA sequencing (RNA-seq) analyses in diverse hybrid varieties resulting from the intergeneric hybridization of goldfish (Carassius auratus red var.) and common carp (Cyprinus carpio). These hybrid individuals were characterized by distinct mitochondrial genomes and copy number variations. Through a weighted gene correlation network analysis, we identified 3693 genes as candidate growth-regulated genes. Among them, the expression of 3672 genes in subgenome R (originating from goldfish) displayed negative correlations with growth rate, whereas 20 genes in subgenome C (originating from common carp) exhibited positive correlations. Notably, we observed intriguing patterns in the expression of slc2a12 in subgenome C, showing opposite correlations with body weight that changed with water temperatures, suggesting differential interactions between feeding activity and weight gain in response to seasonal changes for hybrid animals. In 40.31% of alleles, we observed dominant trans-regulatory effects in the regulatory interaction between distinct alleles from subgenomes R and C. Integrating analyses of allelic-specific expression and DNA methylation data revealed that the influence of DNA methylation on both subgenomes shapes the relative contribution of allelic expression to the growth rate. These findings provide novel insights into the interaction of distinct subgenomes that underlie heterosis in growth traits and contribute to a better understanding of multiple allele traits in animals.

What the hay: predicting equine voluntary forage intake using a meta-analysis approach

To properly formulate diets, the ability to accurately estimate feed intake is critical as the amount of feed consumed will influence the amount of nutrients delivered to the animal. Inaccurate intake estimates may lead to under- or over-feeding of nutrients to the animal. Individual differences in equine forage intake are well-known, but predictive equations based on animal and nutritional factors are not comprehensive. The objective of the present study was to consolidate the current body of knowledge in the published literature on voluntary forage DM intake (VFDMI) in equines and conduct a meta-analysis to identify driving factors, sources of heterogeneity, and develop predictive equations. Therefore, a systematic literature search was applied and identified 61 publications which met the inclusion criteria. From each study, the outcomes of interest (e.g., forage intake), diet composition (e.g., forage information, nutrient composition), and animal factors (e.g., sex, age, breed, BW, exercise level) were extracted. Forage intake was analyzed as two different outcome variables: (1) VFDMI in kg/d and (2) VFDMI in g/kg BW. Linear mixed model analysis treating study as a random effect was applied, using a backward−stepping approach to identifying potential driving variables for VFDMI (both units) where all terms have P < 0.1. The best fitting models for VFDMI included similar factors (also across kg/d and g/kg BW) such as forage quality (i.e., neutral detergent fiber or CP content), forage type (i.e., grass, legume, or mixed), the animals’ size category (i.e., horses vs ponies), and some management factors (i.e., pasture access). As anticipated, forage intake increased when higher quality forages were fed (i.e., lower neutral detergent fiber or higher CP), potentially due to improved digestibility. Additionally, VFDMI increased as BW increased but ponies increased their VFDMI more per every kg increase in BW compared to horses. Lastly, pasture access (i.e., grazing) may influence VFDMI such that pastured animals consume less than stalled animals, possibly due to the time it takes to graze forage. In conclusion, equations to predict equine VFDMI with high accuracy and precision (concordance correlation coefficient = 0.82 – 0.95; root mean squared error RMSE = 0.82–5.49) were developed which could be applied in practice by equine nutritionists or owners and managers. The results of this meta-analysis confirm that animal traits and forage quality have a significant impact on the VFDMI of equines and should be accounted for when formulating diets to ensure nutritional requirements are met.