Beyond the Chicken: Alternative Avian Models for Developmental Physiological Research

Genetic regulation of gene expression across multiple tissues in chickens

The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking. Here, we integrated bulk RNA sequencing (RNA-seq) data from 7,015 samples, single-cell RNA-seq data from 127,598 cells and 2,869 whole-genome sequences to present a pilot atlas of regulatory variants across 28 chicken tissues. This atlas reveals millions of regulatory effects on primary expression (protein-coding genes, long non-coding RNA and exons) and post-transcriptional modifications (alternative splicing and 3'-untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants, their context-dependent behavior and their utility in interpreting genome-wide associations for 39 chicken complex traits. Finally, our comparative analyses of gene regulation between chickens and mammals demonstrate how this resource can facilitate cross-species gene mapping of complex traits.

Respiratory and hematological physiology of day 15 chicken embryos (Gallus gallus domesticus) during water submergence and air recovery: Implications for bird embryos experiencing nest inundation

Bird nests of coastal or inland breeding birds can temporarily flood during high tides or storms. However, respiratory physiological disruption of such water submersion and implications for post-submergence survival are poorly understood. We hypothesized that respiratory physiological disturbances caused by submersion would be rapidly corrected following return to normal gas exchange across the eggshell, thus explaining survival of nest inundation in the field. We further hypothesized that the chicken embryo prior to hatching will develop the ability to recover from acid-base disturbance. We exposed day 15 embryonated chicken eggs (a well-studied point 3/4 through development) to half- or full submersion in water (producing moderate and severe hypoxia, respectively) or in mineral oil (anoxia) for periods of 2-24 h to create varying degrees of submersion-related respiratory and acid-base disturbances. Egg submergence was followed by up to six hours in air to determine the extent and rate of physiological recovery. Arterialized blood PO2 and [lactate], acid-base and hematology were measured at frequent intervals (5 min to 2 h depending on tested variable) both during submersion and air recovery. Submersion in mineral oil - eliminating all gas exchange - proved lethal at two hours. Yet, calculated embryonic oxygen stores suggest submerged embryos should be able to maintain pre-submergence oxygen consumption for only ∼15 mins, suggesting a possibly adaptive immediate decline in metabolism upon submergence. Half- or full submergence in water created blood acid-base disturbances within as little as 5 min, with partial recovery towards the end of 24 h of submergence. Six hours of subsequent air recovery fully restored acid-base homeostasis. Hematological changes that appeared within 5 min of submersion - primarily red blood cell swelling - were eliminated within 1 h following return to air. Importantly, these data indicate a surprising resilience of the chicken embryo to temporary elimination of normal gas exchange which, if evident in other species, provides underlying mechanisms for surviving nest inundation.

The avian embryo as a time-honoured animal model in developmental, biomedical and agricultural research

Avian embryos have been at the core of embryological, morphological, physiological and biochemical/molecular research, especially involving research in three primary areas: developmental, biomedical and agricultural research. As developmental models, the avian embryo-especially that of the chicken-has been the single most used embryo model, perhaps in part from the combination of large size, ease of access and prior knowledge base. Developmental research with avian embryos has included organ system studies of the heart, vasculature, lungs, kidneys, nervous system, etc., as well as integrated physiological processes including gas-exchange, acid-base and ion/water regulation. In terms of translational research, avian embryos have modelled vascular development, based on the easily accessible chorioallantoic membrane under the eggshell. This same respiratory organ has enabled toxicological studies of how pollutants affect vertebrate development. Investigation of the transition to pulmonary breathing and the associated emergence of respiratory control has also relied heavily upon the avian embryo. In addition to developmental and biomedical investigations, the avian embryo has been studied intensively due to the huge importance of domesticated birds as a food source. Consequently, the effects of environment (including temperature, humidity, noise levels and photoperiod) during incubation on subsequent post-hatch phenotype are being actively investigated.This article is part of the theme issue 'The biology of the avian respiratory system'.

Pronounced early differentiation underlies zebra finch gonadal germ cell development

The diversity of germ cell developmental strategies has been well documented across many vertebrate clades. However, much of our understanding of avian primordial germ cell (PGC) specification and differentiation has derived from only one species, the chicken (Gallus gallus). Of the three major classes of birds, chickens belong to Galloanserae, representing less than 4% of species, while nearly 95% of extant bird species belong to Neoaves. This represents a significant gap in our knowledge of germ cell development across avian species, hampering efforts to adapt genome editing and reproductive technologies developed in chicken to other birds. We therefore applied single-cell RNA sequencing to investigate inter-species differences in germ cell development between chicken and zebra finch (Taeniopygia castanotis), a Neoaves songbird species and a common model of vocal learning. Analysis of early embryonic male and female gonads revealed the presence of two distinct early germ cell types in zebra finch and only one in chicken. Both germ cell types expressed zebra finch Germline Restricted Chromosome (GRC) genes, present only in songbirds among birds. One of the zebra finch germ cell types expressed the canonical PGC markers, as did chicken, but with expression differences in several signaling pathways and biological processes. The second zebra finch germ cell cluster was marked by proliferation and fate determination markers, indicating beginning of differentiation. Notably, these two zebra finch germ cell populations were present in both male and female zebra finch gonads as early as HH25. Using additional chicken developmental stages, similar germ cell heterogeneity was identified in the more developed gonads of females, but not males. Overall, our study demonstrates a substantial heterochrony in zebra finch germ cell development compared to chicken, indicating a richer diversity of avian germ cell developmental strategies than previously known.

Responses of Jumbo Quail to a Diet Containing Corticated Marama Bean (Tylosema esculentum) Meal Pre-Treated with Fibrolytic Multi-Enzymes

The nutritional utility of leguminous products such as corticated marama bean (Tylosema esculentum) meal (CMBM) in quail diets is limited by high fibre levels. This study evaluated the impact of dietary CMBM pre-treated with fibrolytic multi-enzyme (FMENZ) on growth performance, and physiological and meat quality responses in Jumbo Coturnix quail. Two hundred and forty 7-day-old Jumbo quail (29.4 ± 2.72 g initial live weight) were randomly distributed to five experimental diets, with six replicate cages each (eight birds/cage). The diets were a grower diet without CMBM, and the same grower diet plus 100 g/kg CMBM pre-treated with 0, 1, 1.5, and 2% (v/w) FMENZ. Positive quadratic responses (p < 0.05) were recorded for overall feed intake and body weight gain in weeks 2 and 3. The control diet promoted the highest (p < 0.05) gain-to-feed ratio in weeks 2 and 3, and the best weight gains and glucose levels, but reduced lipase levels. Final body weights declined linearly [p = 0.037] with FMENZ levels. Breast pH increased linearly, while haemoglobin and 1 h post-mortem chroma showed positive quadratic effects (p < 0.05) with FMENZ levels. The use of the enzymes did not improve the feed value of CMBM in Jumbo quail diets.

PGC-based cryobanking, regeneration through germline chimera mating, and CRISPR/Cas9-mediated TYRP1 modification in indigenous Chinese chickens

Primordial germ cells (PGCs) are vital for producing sperm and eggs and are crucial for conserving chicken germplasm and creating genetically modified chickens. However, efforts to use PGCs for preserving native chicken germplasm and genetic modification via CRISPR/Cas9 are limited. Here we show that we established 289 PGC lines from eight Chinese chicken populations with an 81.6% success rate. We regenerated Piao chickens by repropagating cryopreserved PGCs and transplanting them into recipient chickens, achieving a 12.7% efficiency rate. These regenerated chickens carried mitochondrial DNA from female donor PGC and the rumplessness mutation from both male and female donors. Additionally, we created the TYRP1 (tyrosinase-related protein 1) knockout (KO) PGC lines via CRISPR/Cas9. Transplanting KO cells into male recipients and mating them with wild-type hens produced four TYRP1 KO chickens with brown plumage due to reduced eumelanin production. Our work demonstrates efficient PGC culture, cryopreservation, regeneration, and gene editing in chickens.

The Influence of Cecal Microbiota Transplantation on Chicken Injurious Behavior: Perspective in Human Neuropsychiatric Research

Numerous studies have evidenced that neuropsychiatric disorders (mental illness and emotional disturbances) with aggression (or violence) pose a significant challenge to public health and contribute to a substantial economic burden worldwide. Especially, social disorganization (or social inequality) associated with childhood adversity has long-lasting effects on mental health, increasing the risk of developing neuropsychiatric disorders. Intestinal bacteria, functionally as an endocrine organ and a second brain, release various immunomodulators and bioactive compounds directly or indirectly regulating a host's physiological and behavioral homeostasis. Under various social challenges, stress-induced dysbiosis increases gut permeability causes serial reactions: releasing neurotoxic compounds, leading to neuroinflammation and neuronal injury, and eventually neuropsychiatric disorders associated with aggressive, violent, or impulsive behavior in humans and various animals via a complex bidirectional communication of the microbiota-gut-brain (MGB) axis. The dysregulation of the MGB axis has also been recognized as one of the reasons for the prevalence of social stress-induced injurious behaviors (feather pecking, aggression, and cannibalistic pecking) in chickens. However, existing knowledge of preventing and treating these disorders in both humans and chickens is not well understood. In previous studies, we developed a non-mammal model in an abnormal behavioral investigation by rationalizing the effects of gut microbiota on injurious behaviors in chickens. Based on our earlier success, the perspective article outlines the possibility of reducing stress-induced injurious behaviors in chickens through modifying gut microbiota via cecal microbiota transplantation, with the potential for providing a biotherapeutic rationale for preventing injurious behaviors among individuals with mental disorders via restoring gut microbiota diversity and function.

Interactions between avian viruses and skin in farm birds

This article reviews the avian viruses that infect the skin of domestic farm birds of primary economic importance: chicken, duck, turkey, and goose. Many avian viruses (e.g., poxviruses, herpesviruses, Influenza viruses, retroviruses) leading to pathologies infect the skin and the appendages of these birds. Some of these viruses (e.g., Marek's disease virus, avian influenza viruses) have had and/or still have a devasting impact on the poultry economy. The skin tropism of these viruses is key to the pathology and virus life cycle, in particular for virus entry, shedding, and/or transmission. In addition, for some emergent arboviruses, such as flaviviruses, the skin is often the entry gate of the virus after mosquito bites, whether or not the host develops symptoms (e.g., West Nile virus). Various avian skin models, from primary cells to three-dimensional models, are currently available to better understand virus-skin interactions (such as replication, pathogenesis, cell response, and co-infection). These models may be key to finding solutions to prevent or halt viral infection in poultry.

Peripheral inflammation-induced changes in songbird brain gene expression: 3' mRNA transcriptomic approach

Species-specific neural inflammation can be induced by profound immune signalling from periphery to brain. Recent advances in transcriptomics offer cost-effective approaches to study this regulation. In a population of captive zebra finch (Taeniopygia guttata), we compare the differential gene expression patterns in lipopolysaccharide (LPS)-triggered peripheral inflammation revealed by RNA-seq and QuantSeq. The RNA-seq approach identified more differentially expressed genes but failed to detect any inflammatory markers. In contrast, QuantSeq results identified specific expression changes in the genes regulating inflammation. Next, we adopted QuantSeq to relate peripheral and brain transcriptomes. We identified subtle changes in the brain gene expression during the peripheral inflammation (e.g. up-regulation in AVD-like and ACOD1 expression) and detected co-structure between the peripheral and brain inflammation. Our results suggest benefits of the 3'end transcriptomics for association studies between peripheral and neural inflammation in genetically heterogeneous models and identify potential targets for the future brain research in birds.

Experimental assessment of cardiovascular physiology in the chick embryo

High resolution assessment of cardiac functional parameters is crucial in translational animal research. The chick embryo is a historically well-used in vivo model for cardiovascular research due to its many practical advantages, and the conserved form and function of the chick and human cardiogenesis programs. This review aims to provide an overview of several different technical approaches for chick embryo cardiac assessment. Doppler echocardiography, optical coherence tomography, micromagnetic resonance imaging, microparticle image velocimetry, real-time pressure monitoring, and associated issues with the techniques will be discussed. Alongside this discussion, we also highlight recent advances in cardiac function measurements in chick embryos.

Intra-Amniotic Administration of Cashew Nut (Anacardium occidentale L.) Soluble Extract Improved Gut Functionality and Morphology In Vivo (Gallus gallus)

Cashew nuts are rich in dietary fibers, monounsaturated fatty acids, carotenoids, tocopherols, flavonoids, catechins, amino acids, and minerals that offer benefits for health. However, the knowledge of its effect on gut health is lacking. In this way, cashew nut soluble extract (CNSE) was assessed in vivo via intra-amniotic administration in intestinal brush border membrane (BBM) morphology, functionality, and gut microbiota. Four groups were evaluated: (1) no injection (control); (2) H₂O injection (control); (3) 10 mg/mL CNSE (1%); and (4) 50 mg/mL CNSE (5%). Results related to CNSE on duodenal morphological parameters showed higher Paneth cell numbers, goblet cell (GC) diameter in crypt and villi, depth crypt, mixed GC per villi, and villi surface area. Further, it decreased GC number and acid and neutral GC. In the gut microbiota, treatment with CNSE showed a lower abundance of Bifidobacterium, Lactobacillus, and E. coli. Further, in intestinal functionality, CNSE upregulated aminopeptidase (AP) gene expression at 5% compared to 1% CNSE. In conclusion, CNSE had beneficial effects on gut health by improving duodenal BBM functionality, as it upregulated AP gene expression, and by modifying morphological parameters ameliorating digestive and absorptive capacity. For intestinal microbiota, higher concentrations of CNSE or long-term intervention may be necessary.

Domestication and the comparative embryology of birds

Studies of domesticated animals have greatly contributed to our understanding of avian embryology. Foundational questions in developmental biology were motivated by Aristotle's observations of chicken embryos. By the 19th century, the chicken embryo was at the center stage of developmental biology, but how closely does this model species mirror the ample taxonomic diversity that characterizes the avian tree of life? Here, we provide a brief overview of the taxonomic breadth of comparative embryological studies in birds. We particularly focused on staging tables and papers that attempted to document the timing of developmental transformations. We show that most of the current knowledge of avian embryology is based on Galliformes (chicken and quail) and Anseriformes (duck and goose). Nonetheless, data are available for some ecologically diverse avian subclades, including Struthioniformes (e.g., ostrich, emu) and Sphenisciformes (penguins). Thus far, there has only been a handful of descriptive embryological studies in the most speciose subclade of Aves, that is, the songbirds (Passeriniformes). Furthermore, we found that temporal variances for developmental events are generally uniform across a consensus chronological sequence for birds. Based on the available data, developmental trajectories for chicken and other model species appear to be highly similar. We discuss future avenues of research in comparative avian embryology in light of the currently available wealth of data on domesticated species and beyond.

On the use of body mass measures in severity assessment in laboratory passerine birds

Criteria for assessing the severity of scientific procedures in laboratory rodents include the loss of body mass. However, guidance is limited for passerine birds and application of criteria developed for mammals risks poor welfare decisions. Here, I ask whether, and how, body mass criteria could be incorporated into laboratory welfare assessment of passerines. Passerine birds strategically adjust their body mass to minimise combined mortality risk from starvation and predation. A systematic literature review found that strategic mass changes can be sizeable (sometimes > 10%) even over short timescales. Many aspects of a bird's current or past environment, including husbandry and experimental procedures, may alter perceived starvation or predation risks and thus drive strategic mass change via evolved mechanisms. Therefore, body mass criteria used for rodents may be too stringent for passerines, potentially leading to over-estimated severity. Strategic mass changes might obscure those stemming from experimental interventions yet could also offer insights into whether birds perceive an intervention or altered husbandry as a threat. Mass criteria for severity assessment should be species- and context-specific in order to balance needs for refinement and reduction. To guide the development of appropriate criteria, a future research priority is for greater data collection and sharing based on standardised routine monitoring of mass variation under a representative range of husbandry conditions and procedures.

Physiological Regulation of Growth, Hematology and Blood Gases in Chicken Embryos in Response to Low and High Incubation Humidity

Variations from a relative humidity (RH) of ∼50-60% can unfavorably alter chicken embryo development, but little is known of whether the embryo can mitigate these effects through physiological regulation. We examined effects of Low RH (25-35%), and High RH (85-93%) compared to Control RH (50-60%) on hatchability, embryonic growth, hematology and blood gases and pH. Mean hatchability was not affected by RH. Yet, Low RH decreased wet body mass of advanced embryos (days 17-19; d17-19), with lowered body water content compared with embryos of Control and High RH. However, dry body mass of developing (d11-19) embryos was not different between the three RH groups. Mean blood osmolality across development was higher in Low RH embryos and lower in High RH embryos compared with Control embryos. Mean blood lactate was higher in both Low and High RH embryos compared to Control embryos. Unexpectedly, hematological respiratory variables (Hct, [RBC], MCV, [Hb]) and blood gas variables (Po₂, Pco₂, pH, [HCO₃ ^-]) across development were not affected by RH. Mean wet body mass at hatch (d20-22) was larger in High RH embryos compared with Low RH embryos, but mean wet and dry body mass upon euthanasia on d22 was unaffected. The ability of the three populations to physiologically regulate blood respiratory variables and blood acid-base balance was then examined by observing their responses to intrinsic hypoxemia and hypercapnia created by controlled partial egg submersion in water. Hct and [RBC] responses were less disturbed by submersion in High RH embryos compared with both Control and Low RH embryos, which showed major disturbance. Acid-base regulatory responses did not differ between RH groups. We conclude that, while different incubation RHs cause large differences in tissue water content and body mass, most hematological and acid-base regulatory capabilities are regulated near Control values.

Genetically modified mice for research on human diseases: A triumph for Biotechnology or a work in progress?

Genetically modified mice are engineered as models for human diseases. These mouse models include inbred strains, mutants, gene knockouts, gene knockins, and ‘humanized’ mice. Each mouse model is engineered to mimic a specific disease based on a theory of the genetic basis of that disease. For example, to test the amyloid theory of Alzheimer’s disease, mice with amyloid precursor protein genes are engineered, and to test the tau theory, mice with tau genes are engineered. This paper discusses the importance of mouse models in basic research, drug discovery, and translational research, and examines the question of how to define the “best” mouse model of a disease. The critiques of animal models and the caveats in translating the results from animal models to the treatment of human disease are discussed. Since many diseases are heritable, multigenic, age-related and experience-dependent, resulting from multiple gene-gene and gene-environment interactions, it will be essential to develop mouse models that reflect these genetic, epigenetic and environmental factors from a developmental perspective. Such models would provide further insight into disease emergence, progression and the ability to model two-hit and multi-hit theories of disease. The summary examines the biotechnology for creating genetically modified mice which reflect these factors and how they might be used to discover new treatments for complex human diseases such as cancers, neurodevelopmental and neurodegenerative diseases.

Towards Tabula Gallus

The Tabula Gallus is a proposed project that aims to create a map of every cell type in the chicken body and chick embryos. Chickens (Gallus gallus) are one of the most recognized model animals that recapitulate the development and physiology of mammals. The Tabula Gallus will generate a compendium of single-cell transcriptome data from Gallus gallus, characterize each cell type, and provide tools for the study of the biology of this species, similar to other ongoing cell atlas projects (Tabula Muris and Tabula Sapiens/Human Cell Atlas for mice and humans, respectively). The Tabula Gallus will potentially become an international collaboration between many researchers. This project will be useful for the basic scientific study of Gallus gallus and other birds (e.g., cell biology, molecular biology, developmental biology, neuroscience, physiology, oncology, virology, behavior, ecology, and evolution). It will eventually be beneficial for a better understanding of human health and diseases.