Genes for resilience to heat stress in small ruminants: A review

Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits

BACKGROUND

Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS).

RESULTS

In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits.

CONCLUSIONS

The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.

Metabolic profile and gene expression pattern of cytokines and antioxidants markers during different physiological stages in Barki ewes

BACKGROUND

In livestock, identifying the physiological and reproductive stages is valuable in guiding management decisions related to nutrition, veterinary procedures, and breeding programs. To achieve this goal, a cohort of Barki ewes in this research underwent observation across three pivotal physiological conditions: pre-pregnancy, late pregnancy, and early lactation. Blood samples were collected to investigate the changes in serum metabolic profile as well as gene expression pattern of cytokines and antioxidants markers during these stages.

RESULTS

Our results showed that during late pregnancy, there was a significant (P < 0.05) increase in red blood cells (11.9 ± 0.5 1012/L), hemoglobin (10.8 ± 0.4 g/dl) and neutrophils count (7 ± 0.1 109/L) with significant decrease (P < 0.05) of total white blood cell count (9.1 ± 0.05 109/L). The packed cell volume (%) and monocyte count showed a significant (P < 0.05) decrease during both late pregnancy and early lactation stages. The serum concentrations of glucose, cholesterol, GSH, GPx, SOD and catalase displayed significant (P < 0.05) decrease during late pregnancy and early-lactation. Notably, during late pregnancy, there was a significant (P < 0.05) increase in the serum concentrations of albumin, globulin, urea, IGF-1, and malondialdehyde with significant decrease (P < 0.05) of total protein (4.9 ± 0.08 g/dl). Additionally, during early lactation, there was a significant (P < 0.05) increase in the serum levels of non-esterified fatty acids, triiodothyronine (T3), and thyroxin (T4). The gene expression profiles of cytokines (IL-4, IL-6, IL-8, and NFKB) were decreased in the ewes during late pregnancy compared to pre-pregnant and early lactation stages. In addition, the expression profile of antioxidant genes (SOD, CAT, GPX, and Nrf2) was significantly upsurged in the non-pregnant ewes compared to late pregnancy and early lactation ones.

CONCLUSIONS

The results concluded that different physiological status significantly affects the blood metabolic profile and gene expression pattern in Barki sheep. Our findings can be helpful in monitoring animal health and applying in breeding programs of Barki sheep under harsh environmental conditions.

Exploring genetic variation in potential indicators of resilience in sheep using fibre diameter measured along the wool staple

Production animals are increasingly exposed to a wide variety of disturbances that can compromise their productivity, health and well-being. As a result, there is a growing need to be able to select animals that are more resilient to environmental disturbances. Fibre diameter variation measured along a wool staple is expected to contain information about how resilient sheep are to the disturbances of their internal and external environment. This study aimed to develop potential resilience indicators from fibre diameter variation, estimate their genetic parameters and assess whether these traits are genetically correlated across three age stages. The study used 6 140 Merino sheep from the Sheep Cooperative Research Centre Information Nucleus Flocks recorded at yearling, 2 years old, and adult ages. Eight potential traits were defined based on theory, literature and exploratory analysis, which were suggested to capture the animal's ability to resist, respond and recover from potential disturbances. Genetic evaluation of the traits was conducted using pedigree-based animal models. The traits were shown to be low to moderately heritable (0.01-0.33) when examined at each of the three age stages. The potential indicators were generally well correlated with one another within age stages. Further, the genetic correlation between the same trait measured at different age stages was moderate to high between yearling and 2 years old (0.35-0.94) and between 2 years old and adults (0.18-0.70), while slightly lower between yearling and adult estimates (0.09-0.62). These results suggest that selection for resilience indicators from fibre diameter is possible; however, further studies are warranted to refine the trait definitions and validate these indicators against other measures of health, fitness and productive performance.

TRPM4 gene variation associated with climatic conditions in Chinese cattle

The transient receptor potential (TRP) superfamily has been reported to play an important role in heat tolerance pathways. Based on the Bovine Genome Variation Database and Selective Signatures, a missense mutation (NC_037345.1: c.2237A > G: p. His746Arg) (rs209689836) was identified in the transient receptor potential cation channel subfamily M member 4 (TRPM4) gene, a member of the TRP family, corresponding to heat tolerance. Here, we explored the prevalence of this variant in 19 native Chinese cattle (comprised of 404 individuals) to determine its possible association with heat tolerance in Chinese cattle by using PCR and DNA sequencing. The distribution of alleles of NC_037345.1: c.2237A > G: p. His746Arg displays significant geographical differences across native Chinese cattle breeds, consistent with the distribution of indicine and taurine cattle in China. Additionally, the association analysis indicated that the G allele was significantly associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (p < .05), suggesting that cattle carrying allele G were distributed in regions with higher T, RH, and THI. In conclusion, our results suggested that the mutation of the TRPM4 gene in Chinese cattle might be a candidate locus associated with heat tolerance.

Differentiation of Hair Sheep Breeds Based on the Physiological and Blood Biochemical Changes in Response to Different Stressors Using Multivariate Analysis Techniques

Physiological and blood measurement changes due to high heat load, restricted feed intake, and limited drinking water availability in 135 animals of three hair sheep breeds (Dorper, Katahdin, and St. Croix) were subjected to multivariate analysis techniques. The objective of this analysis was to evaluate the ability of these variables to separate individual hair sheep into groups based on adaptation characteristics in response to three physiological stressors and identify variables with greater discriminatory power. There were 16, 8, and 13 physiological and blood variables obtained from high heat load, restricted feed consumption, and water intake studies, respectively, for multivariate analysis. Physiological variables such as respiration rate, rectal and skin temperature, and panting score were measured only in the heat stress study. The results of the cluster and canonical discriminant analyses showed the presence of wide divergence (p < 0.05) between St. Croix and other breeds in their responses to high heat loads and restricted-feed- and -water-intake conditions. Dorper and Katahdin were grouped (p > 0.05) together based on the changes in physiological variables, which were separated (p < 0.05) from those of St. Croix as a resilient group. The stepwise discriminant analysis indicated that skin temperature, panting score, rectal temperature, respiration rate, and blood urea nitrogen and oxygen concentrations were the significant (p < 0.05) discriminating variables in clustering individual sheep into groups based on their responses to the high-heat-stress condition. Under the limited feed intake condition, the significant (p < 0.05) traits responsible for the separation of St. Croix from Dorper and Katahdin were blood triglyceride and cholesterol concentrations, whereas blood hemoglobin, osmolality, protein, and albumin were most important discriminating variables under the limited water intake condition. In conclusion, the results of the present study suggest that the stress responses of Dorper and Katahdin are similar and different from that of St. Croix. This finding can be useful information for future decisions in developing climate-resilient sheep through selective breeding.

Thermal stress index for native sheep

The first objective of this study was to develop a thermal stress index for sheep based on environmental and animal data collected in a climate chamber under various environmental conditions. The second objective was to compare published indices of thermal comfort and the proposed index, testing them with the data from this study, with the objective of pointing out the most adequate index to be used by breeders when choosing management procedures. A total of 3024 data were obtained for the physiological variables of the sheep exposed to the eight thermal conditions in the climatic chamber and in ambient condition, kept three days in each thermal condition. A principal component analysis summarized the measurements of physiological variables into only one variable (y1). Using SigmaPlot software, multiple regression of y1 with the environmental variables and their combinations produced a number of indices. The equation chosen was the heat stress index for sheep, TSI = 24.153 - (0.0523*A_T) + (0.746*B_GT) + (4.104*Vp), with R² = 0.668. The correlations presented high values, where these correlation values were assumed to indicate the efficiency of each index as indicators of the animals' response to the environment. Thus, it was assumed that the TSI presents a high efficiency.

Morphology of coat and skin of small ruminants reared in the Brazilian semi-arid region

The structure of the coat and integument of small ruminants reared in semi-arid regions have valuable characteristics that favor their adaptation to the region. The objective of this study was to evaluate the structural characteristics of the coat and integument and sweating capacity of goats and sheep in the Brazilian semi-arid region, using 20 animals, 10 of each breed, 5 males and 5 females of each species, grouped in a completely randomized design in a 2 x 2 factorial scheme (2 species and 2 genders) with 5 replicates. The animals were already being kept under the influence of high temperatures and levels of direct solar radiation before the day of the collections. At the time of the evaluations, ambient temperature was high, with low relative humidity. The pattern of epidermal thickness and sweat glands per body region was superior in sheep (P < 0.05), and the number of hair follicles and sweat rate were similar (P > 0.05) between the species. There was no difference (P > 0.05) in the evaluated characteristics between the genders, showing that they are not influenced by hormones. The morphology of the coat and skin of these animals showed a superiority of goats compared to sheep.

Natural adaptation and human selection of northeast African sheep genomes

African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ∼54× for 130 samples (Ethiopia, Libya) and ∼20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.

Effects of dietary supplementation with alpha-lipoic acid on apparent digestibility and serum metabolome alterations of sheep in summer

To investigate the effects of alpha-lipoic acid (LA) on the nutrition metabolism of sheep (36.72 ± 1.44 kg) in the summer, twenty-one sheep were randomly assigned to three treatments addressing LA supplementation: 0.00 (CTL), 600 (LA-L), and 900 (LA-H) mg/kg of dry matter (DM) per day for each sheep. Whole feces and urine collection methods were used to analyze apparent digestibility; ELISA kits to determine the hormones, antioxidant, and immune parameters in the blood; and serum metabolomics to detect and analyze small molecular substances. The results showed the DM intakes in the LA-L and LA-H groups were significantly increased by 8.22% and 8.02%, respectively, compared to that in the CTL group, and there was no significant effect on average daily gain, feed conversion ratio, nitrogen digestibility, calcium digestibility, and phosphorus digestibility. Regarding hormones, antioxidant, and immune indicators, the concentrations of triiodothyronine, superoxide dismutase, glutathione reductase, HSP70, and IgA significantly increased after LA supplementation, while adrenaline and malondialdehyde levels significantly decreased. With the pairwise comparison of the three groups, metabolomics analysis identified 22 differential metabolites in the positive/negative modes, respectively, which suggested LA supplementation can significantly affect sheep's lipid, amino acid, and nucleic acid metabolism. Additionally, 3-indolepropionic acid, cinnamoylglycine, butyric acid, dodecanedioic acid, indoxyl sulfate, and pantothenic acid were the common differential metabolites with higher concentrations after LA supplementation. In summary, dietary supplementation of LA can increase the sheep's DMI, energy digestibility, antioxidant capacity, and immunity. These changes provide evidence to support the use of LA supplementation for livestock.

Effects of Purple Corn Anthocyanin on Blood Biochemical Indexes, Ruminal Fluid Fermentation, and Rumen Microbiota in Goats

The objective of this study was to observe the effects of anthocyanin from purple corn on blood biochemical indexes, ruminal fluid fermentation parameters, and the microbial population in goats. A total of 18 Qianbei Ma wether kids (body weight, 21.38 ± 1.61 kg; mean ± standard deviation) were randomly assigned to three groups using a completely randomized design. The group diets were: (1) control, basal diet, (2) treatment 1 (LA), basal diet with 0.5-g/d purple corn pigment (PCP), and (3) treatment 2 (HA), basal diet with 1-g/d PCP. The results showed that supplementation of PCP anthocyanin increased (P < 0.05) crude protein and gross energy digestibilities compared to the control. Compared to the control group, the inclusion of anthocyanin-rich PCP led to significantly increased (P < 0.05) plasma reduced glutathione and peroxidase concentrations. Goats receiving PCP had increased (P < 0.05) ruminal fluid acetic acid and a higher ratio of acetate to propionate, while the propionic acid, butyric acid, valeric acid, isobutyric acid, and isovaleric acid levels had decreased (P < 0.05). There was no significant difference (P > 0.05) in ruminal fluid alpha bacterial diversity among the three groups. At the phylum level, the feeding of PCP had significant effect (P < 0.05) on the abundances of Actinobacteriota, Proteobacteria, Elusimicrobiota, WPS-2, and Cyanobacteria. At the genus level, HA group had lower (P < 0.05) Prevotellaceae_NK3B31_group abundance compared to the other groups. In addition, significant differences (P < 0.05) were also observed for the ruminal fluid Eubacterium_nodatum_group, Amnipila, Ruminiclostridium, U29-B03, unclassified_c_Clostridia, Pyramidobacter, Anaeroplasma, UCG-004, Atopobium, norank_f_norank_o_Bradymonadales, Elusimicrobium, norank_f_norank_o_norank_c_norank_p_WPS-2, norank_f_Bacteroidales_UCG-001, and norank_f_norank_o_Gastranaerophilales among all groups. Taken together, the inclusion of anthocyanin-rich PCP increased the antioxidant potential, improved rumen volatile fatty acids, and induced a shift in the structure and relative abundance of ruminal microbiota in growing goats.

Emerging Genetic Tools to Investigate Molecular Pathways Related to Heat Stress in Chickens: A Review

Simple Summary

New genomic tools have been used as an instrument in order to assess the molecular pathway involved in heat stress resistance. Local chicken breeds have a better attitude to face heat stress. This review aims to summarize studies linked to chickens, heat stress, and heat shock protein.

Abstract

Chicken products are the most consumed animal-sourced foods at a global level across greatly diverse cultures, traditions, and religions. The consumption of chicken meat has increased rapidly in the past few decades and chicken meat is the main animal protein source in developing countries. Heat stress is one of the environmental factors which decreases the productive performance of poultry and meat quality. Heat stress produces the over-expression of heat shock factors and heat shock proteins in chicken tissues. Heat shock proteins regulate several molecular pathways in cells in response to stress conditions, changing the homeostasis of cells and tissues. These changes can affect the physiology of the tissue and hence the production ability of chickens. Indeed, commercial chicken strains can reach a high production level, but their body metabolism, being comparatively accelerated, has poor thermoregulation. In contrast, native backyard chickens are more adapted to the environments in which they live, with a robustness that allows them to survive and reproduce constantly. In the past few years, new molecular tools have been developed, such as RNA-Seq, Single Nucleotide Polymorphisms (SNPs), and bioinformatics approaches such as Genome-Wide Association Study (GWAS). Based on these genetic tools, many studies have detected the main pathways involved in cellular response mechanisms. In this context, it is necessary to clarify all the genetic and molecular mechanisms involved in heat stress response. Hence, this paper aims to review the ability of the new generation of genetic tools to clarify the molecular pathways associated with heat stress in chickens, offering new perspectives for the use of these findings in the animal breeding field.

Omics Insights into Animal Resilience and Stress Factors

Resilience is conceived as a dynamic developmental process involving the achievement of positive adaptation within the context of significant adversity. Resilience is not a unique ability but rather a set of capacities of a system put in place to absorb a disturbance and to reorganize while trying to retain the same function, structure, and identity. This review describes the characteristics and the molecular mechanisms of resilience to understand the core elements of resilience and its indicators. The objectives of this review are: (1) to define some of the leading environmental stressors and clarify the mechanism of vulnerability or resilience outcomes; (2) to clarify some of the prominent epigenetic modulations mediating resilience or vulnerability as a stress response; (3) to highlight the neural mechanisms related to stress resilience since the central nervous system is a highly dynamic structure characterized by an everlasting plasticity feature, which therefore has the opportunity to modify resilience. The review aims to introduce the reader to the concept of resilience seen as an ability acquired in life and not only inherited from birth.

Non-Invasive Sheep Biometrics Obtained by Computer Vision Algorithms and Machine Learning Modeling Using Integrated Visible/Infrared Thermal Cameras

Live sheep export has become a public concern. This study aimed to test a non-contact biometric system based on artificial intelligence to assess heat stress of sheep to be potentially used as automated animal welfare assessment in farms and while in transport. Skin temperature (°C) from head features were extracted from infrared thermal videos (IRTV) using automated tracking algorithms. Two parameter engineering procedures from RGB videos were performed to assess Heart Rate (HR) in beats per minute (BPM) and respiration rate (RR) in breaths per minute (BrPM): (i) using changes in luminosity of the green (G) channel and (ii) changes in the green to red (a) from the CIELAB color scale. A supervised machine learning (ML) classification model was developed using raw RR parameters as inputs to classify cutoff frequencies for low, medium, and high respiration rate (Model 1). A supervised ML regression model was developed using raw HR and RR parameters from Model 1 (Model 2). Results showed that Models 1 and 2 were highly accurate in the estimation of RR frequency level with 96% overall accuracy (Model 1), and HR and RR with R = 0.94 and slope = 0.76 (Model 2) without statistical signs of overfitting.

Characterization of immunological, biochemical and inflammatory response of clinical and subclinical endometritis in ewes in the subtropics

Pluriparus Ossimi (n = 50) ewes were used to investigate the immune profile of the affected ewes to accurately diagnose clinical and subclinical endometritis and associations with biochemical variables. Ewes were slaughtered and animals were classified into control (no fertility problems), subclinical endometritis (SCE) and clinical endometritis (CE) groups based on pre-slaughter determinations of conception failure. Serum was collected from ewes to estimate concentrations of pro-inflammatory cytokines including interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) and interleukin-8 (IL-8) as well as nitric oxide (NO) concentration. The results from immunological evaluations indicated there were greater (P < 0.001) serum concentrations of IL-6, IL-8, TNF-α and NO in ewes classified with SCE and CE as compared to ewes of the control group. Furthermore, values for concentrations of TNF-α were positively correlated with IL-6 and IL-8 concentrations in ewes of the SCE and CE groups. In ewes classified with CE and SCE there were greater (P < 0.01) concentrations of blood glucose, ALT, AST, urea and creatinine than in ewes of the control group. It is concluded that serum pro-inflammatory cytokines IL-6, IL-8, and TNF-α are diagnostic markers for CE and SCE in ewes and serve as a criterion for different inflammatory complications in ewes classified as having CE or SCE.

Genetic Selection for Thermotolerance in Ruminants

Variations in climatic variables (temperature, humidity and solar radiation) negatively impact livestock growth, reproduction, and production. Heat stress, for instance, is a source of huge financial loss to livestock production globally. There have been significant advances in physical modifications of animal environment and nutritional interventions as tools of heat stress mitigation. Unfortunately, these are short-term solutions and may be unsustainable, costly, and not applicable to all production systems. Accordingly, there is a need for innovative, practical, and sustainable approaches to overcome the challenges posed by global warming and climate change-induced heat stress. This review highlights attempts to genetically select and breed ruminants for thermotolerance and thereby sustain production in the face of changing climates. One effective way is to incorporate sustainable heat abatement strategies in ruminant production. Improved knowledge of the physiology of ruminant acclimation to harsh environments, the opportunities and tools available for selecting and breeding thermotolerant ruminants, and the matching of animals to appropriate environments should help to minimise the effect of heat stress on sustainable animal genetic resource growth, production, and reproduction to ensure protein food security.

Prediction models, assessment methodologies and biotechnological tools to quantify heat stress response in ruminant livestock

Livestock industries have an important role in ensuring global food security. This review discusses the importance of quantifying the heat stress response of ruminants, with an emphasis on identifying thermo-tolerant breeds. There are numerous heat stress prediction models that have attempted to quantify the response of ruminant livestock to hot climatic conditions. This review highlights the importance of investigating prediction models beyond the temperature-humidity index (THI). Furthermore, this review highlights the importance of incorporating other climatic variables when developing prediction indices to ensure the accurate prediction of heat stress in ruminants. Prediction models, particularly the heat load index (HLI) were developed to overcome the limitations of the THI by incorporating ambient temperature (AT), relative humidity (RH), solar radiation (SR) and wind speed (WS). Furthermore refinements to existing prediction models have been undertaken to account for the interactions between climatic variables and physiological traits of livestock. Specifically, studies have investigated the relationships between coat characteristics, respiration rate (RR), body temperature (BT), sweating rate, vasodilation, body weight (BW), body condition score (BCS), fatness and feed intake with climatic conditions. While advancements in prediction models have been occurring, there has also been substantial advancement in the methodologies used to quantify animal responses to heat stress. The most recent development in this field is the application of radio frequency identification (RFID) technology to record animal behaviour and various physiological responses. Rumen temperature measurements using rumen boluses and skin temperature recording using infrared thermography (IRT) are making inroads to redefine the quantification of the heat stress response of ruminants. Further, this review describes several advanced biotechnological tools that can be used to identify climate resilient breeds of ruminant livestock.