Differential expression of microRNAs associated with thermal stress in Frieswal (Bos taurus x Bos indicus) crossbred dairy cattle

Effect of access to natural shade on scrotal thermoregulatory capacity, integrity of the testicular parenchyma and sperm morphology of Nelore (Bos indicus) and Canchim (Bos taurus x Bos indicus) bulls

The objective of this work was to evaluate the effect of using naturally shaded pastures on scrotal thermoregulatory capacity, testicular echotexture, and sperm morphology of Nelore (Bos indicus) and Canchim (5/8 Bos taurus x 3/8 Bos indicus) bulls in a tropical climate region. Sixty-four adult Nelore and Canchim bulls were used, equally allocated in Full Sun (FS, n = 32) or Crop-Livestock-Forestry (CLF, n = 32) pasture systems. During five consecutive climate seasons, the bulls underwent monthly breeding soundness evaluations and the biometeorological variables in the systems were continuously monitored. Microclimate was significantly different between systems. CLF system had lower BGHI than FS throughout the experimental period. No triple interaction (Season x Breed x Treatment, P > 0.05) was observed for any of the variables. Animals in CLF showed lower body temperature in Summer (FS:39.41 ± 0.05 vs. CLF:39.30 ± 0.05 °C; P = 0.005) and in Autumn (FS:39.54 ± 0.05 vs. CLF:39.35 ± 0.05 °C; P = 0.005). Access to shading did not determine differences in the evolution of scrotal biometry, temperatures, and scrotal thermal gradients (P > 0.05). Regardless of breed, animals in CLF showed greater right testicular volume (FS:247.5 ± 5.7 vs. CLF:259.0 ± 5.7 cm³; P < 0.05), more suitable parenchyma echotexture, and fewer microlithiasis spots in the Spring and Summer. Testosterone concentration was higher in FS (FS:2.6 ± 0.2 vs. CLF:2.1 ± 0.2 ng/mL; P = 0.035). Canchim bulls presented higher total sperm defects during the Autumn and Winter (P = 0.010), but the total defects levels for Canchim and Nelore bulls were in normal range for adult bulls. Thus, the natural shade in CLF system was effective in improving the microclimate of pastures and minimizing adverse environmental effects on some reproductive features of interest in beef cattle.

Differential Hepatic Expression of miRNA in Response to Aflatoxin B1 Challenge in Domestic and Wild Turkeys

Aflatoxin B1 (AFB1) is a major foodborne mycotoxin that poses a significant economic risk to poultry due to a greater degree of susceptibility compared to other agricultural species. Domesticated turkeys (Meleagris gallopavo) are especially sensitive to AFB1; however, wild turkeys (M. g. silvestris) are more resistant. A lack of functional isoforms of hepatic glutathione S-transferases (GSTs), an enzyme that plays a role in the detoxification of aflatoxin, is suspected as the reason for the increased sensitivity. Previous studies comparing the gene expression of domesticated and wild turkeys exposed to AFB1 identified hepatic genes responding differentially to AFB1, but could not fully explain the difference in response. The current study examined differences in the expression of microRNAs (miRNAs) in the livers of wild and domesticated turkeys fed dietary AFB1 (320 μg/kg in feed). Short-read RNA sequencing and expression analysis examined both domesticated and wild turkeys exposed to AFB1 compared to controls. A total of 25 miRNAs was identified as being significantly differentially expressed (DEM) in pairwise comparisons. The majority of these have mammalian orthologs with known dysregulation in liver disease. The largest number of DEMs occurred between controls, suggesting an underlying difference in liver potential. Sequences of the DEMs were used to identify potential miRNA binding sites in target genes, resulting in an average of 4302 predicted target sites per DEM. These DEMs and gene targets provide hypotheses for future investigations into the role of miRNAs in AFB1 resistance.

microRNA Temporal-Specific Expression Profiles Reveal longissimus dorsi Muscle Development in Tianzhu White Yak

As a class of regulatory factors, microRNAs (miRNAs) play an important role in regulating normal muscle development and fat deposition. Muscle and adipose tissues, as major components of the animal organism, are also economically important traits in livestock production. However, the effect of miRNA expression profiles on the development of muscle and adipose tissues in yak is currently unknown. In this study, we performed RNA sequencing (RNA-Seq) on Tianzhu white yak longissimus dorsi muscle tissue obtained from calves (6 months of age, M6, n = 6) and young (30 months of age, M30, n = 6) and adult yak (54 months of age, M54, n = 6) to identify which miRNAs are differentially expressed and to investigate their temporal expression profiles, establishing a regulatory network of miRNAs associated with the development of muscle and adipose. The results showed that 1191 miRNAs and 22061 mRNAs were screened across the three stages, of which the numbers of differentially expressed miRNAs (DE miRNAs) and differentially expressed mRNAs (DE mRNAs) were 225 and 450, respectively. The expression levels of the nine DE miRNAs were confirmed using a reverse transcription quantitative PCR (RT-qPCR) assay, and the trend of the assay results was generally consistent with the trend of the transcriptome profiles. Based on the expression trend, DE miRNAs were categorized into eight different expression patterns. Regarding the expression of DE miRNAs in sub-trends Profile 1 and Profile 2 (p < 0.05), the gene expression patterns were upregulated (87 DE miRNAs). Gene ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG) analyses showed that the identified DE miRNAs and DE mRNAs were enriched in pathway entries associated with muscle and intramuscular fat (IMF) growth and development. On this basis, we constructed a DE miRNA-mRNA interaction network. We found that some DE mRNAs of interest overlapped with miRNA target genes, such as ACSL3, FOXO3, FBXO30, FGFBP4, TSKU, MYH10 (muscle development), ACOX1, FADS2, EIF4E2, SCD1, EL0VL5, and ACACB (intramuscular fat deposition). These results provide a valuable resource for further studies on the molecular mechanisms of muscle tissue development in yak and also lay a foundation for investigating the interactions between genes and miRNAs.

Proteomic changes of the bovine blood plasma in response to heat stress in a tropically adapted cattle breed

Background

Identifying molecular mechanisms responsible for the response to heat stress is essential to increase production, reproduction, health, and welfare. This study aimed to identify early biological responses and potential biomarkers involved in the response to heat stress and animal's recovery in tropically adapted beef cattle through proteomic analysis of blood plasma.

Methods

Blood samples were collected from 14 Caracu males during the heat stress peak (HSP) and 16 h after it (heat stress recovery-HSR) assessed based on wet bulb globe temperature index and rectal temperature. Proteome was investigated by liquid chromatography-tandem mass spectrometry from plasma samples, and the differentially regulated proteins were evaluated by functional enrichment analysis using DAVID tool. The protein-protein interaction network was evaluated by STRING tool.

Results

A total of 1,550 proteins were detected in both time points, of which 84 and 65 were downregulated and upregulated during HSR, respectively. Among the differentially regulated proteins with the highest absolute log-fold change values, those encoded by the GABBR1, EPHA2, DUSP5, MUC2, DGCR8, MAP2K7, ADRA1A, CXADR, TOPBP1, and NEB genes were highlighted as potential biomarkers because of their roles in response to heat stress. The functional enrichment analysis revealed that 65 Gene Ontology terms and 34 pathways were significant (P < 0.05). We highlighted those that could be associated with the response to heat stress, such as those related to the immune system, complement system, hemostasis, calcium, ECM-receptor interaction, and PI3K-Akt and MAPK signaling pathways. In addition, the protein-protein interaction network analysis revealed several complement and coagulation proteins and acute-phase proteins as important nodes based on their centrality and edges.

Conclusion

Identifying differentially regulated proteins and their relationship, as well as their roles in key pathways contribute to improve the knowledge of the mechanisms behind the response to heat stress in naturally adapted cattle breeds. In addition, proteins highlighted herein are potential biomarkers involved in the early response and recovery from heat stress in tropically adapted beef cattle.

Genome-wide DNA methylation profiles regulate distinct heat stress response in zebu (Bos indicus) and crossbred (Bos indicus × Bos taurus) cattle

Epigenetic variations result from long-term adaptation to environmental factors. The Bos indicus (zebu) adapted to tropical conditions, whereas Bos taurus adapted to temperate conditions; hence native zebu cattle and its crossbred (B indicus × B taurus) show differences in responses to heat stress. The present study evaluated genome-wide DNA methylation profiles of these two breeds of cattle that may explain distinct heat stress responses. Physiological responses to heat stress and estimated values of Iberia heat tolerance coefficient and Benezra's coefficient of adaptability revealed better relative thermotolerance of Hariana compared to the Vrindavani cattle. Genome-wide DNA methylation patterns were different for Hariana and Vrindavani cattle. The comparison between breeds indicated the presence of 4599 significant differentially methylated CpGs with 756 hypermethylated and 3845 hypomethylated in Hariana compared to the Vrindavani cattle. Further, we found 79 genes that showed both differential methylation and differential expression that are involved in cellular stress response functions. Differential methylations in the microRNA coding sequences also revealed their functions in heat stress responses. Taken together, epigenetic differences represent the potential regulation of long-term adaptation of Hariana (B indicus) cattle to the tropical environment and relative thermotolerance.

Validation of Selected MicroRNA Transcriptome Data in the Bovine Corpus Luteum during Early Pregnancy by RT-qPCR

In cattle, the corpus luteum (CL) is pivotal in maintaining early pregnancy by secreting progesterone. To establish pregnancy, the conceptus produces interferon-τ, preventing luteolysis and initiating the transformation of the CL spurium into a CL verum. Although this transformation is tightly regulated, limited data are available on the expression of microRNAs (miRNAs) during and after this process. To address this gap, we re-analyzed previously published RNA-Seq data of CL from pregnant cows and regressed CL from non-pregnant cows. This analysis identified 44 differentially expressed miRNAs. From this pool, three miRNAs-bta-miR-222-3p, bta-miR-29c, and bta-miR-2411-3p-were randomly selected for relative quantification. Using bovine ovaries (n = 14) obtained from an abattoir, total RNA (including miRNAs) was extracted and converted to cDNA for RT-qPCR. The results revealed that bta-miR-222-3p was downregulated (p = 0.016) in pregnant females compared to non-pregnant cows with regressed CL. However, no differences in miRNA expression were observed between CL of pregnant and non-pregnant cows for bta-miR-29c (p > 0.32) or bta-miR-2411-3p (p > 0.60). In silico prediction approaches indicated that these miRNAs are involved in pathways regulating pregnancy maintenance, such as the VEGF- and FoxO-signaling pathways. Additionally, their biogenesis is regulated by GABPA and E2F4 transcription factors. The validation of selected miRNA expression in the CL during pregnancy by RT-qPCR provides novel insights that could potentially lead to the identification of biomarkers related to CL physiology and pregnancy outcome.

Unravelling the impact of epigenetic mechanisms on offspring growth, production, reproduction and disease susceptibility

Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNA molecules, play a critical role in gene expression and regulation in livestock species, influencing development, reproduction and disease resistance. DNA methylation patterns silence gene expression by blocking transcription factor binding, while histone modifications alter chromatin structure and affect DNA accessibility. Livestock-specific histone modifications contribute to gene expression and genome stability. Non-coding RNAs, including miRNAs, piRNAs, siRNAs, snoRNAs, lncRNAs and circRNAs, regulate gene expression post-transcriptionally. Transgenerational epigenetic inheritance occurs in livestock, with environmental factors impacting epigenetic modifications and phenotypic traits across generations. Epigenetic regulation revealed significant effect on gene expression profiling that can be exploited for various targeted traits like muscle hypertrophy, puberty onset, growth, metabolism, disease resistance and milk production in livestock and poultry breeds. Epigenetic regulation of imprinted genes affects cattle growth and metabolism while epigenetic modifications play a role in disease resistance and mastitis in dairy cattle, as well as milk protein gene regulation during lactation. Nutri-epigenomics research also reveals the influence of maternal nutrition on offspring's epigenetic regulation of metabolic homeostasis in cattle, sheep, goat and poultry. Integrating cyto-genomics approaches enhances understanding of epigenetic mechanisms in livestock breeding, providing insights into chromosomal structure, rearrangements and their impact on gene regulation and phenotypic traits. This review presents potential research areas to enhance production potential and deepen our understanding of epigenetic changes in livestock, offering opportunities for genetic improvement, reproductive management, disease control and milk production in diverse livestock species.

Heat stress adaptation in cows - Physiological responses and underlying molecular mechanisms

Heat stress is a key abiotic stressor for dairy production in the tropics which is further compounded by the ongoing climate change. Heat stress not only adversely impacts the production and welfare of dairy cows but severely impacts the economics of dairying due to production losses and increased cost of rearing. Over the years, selection has ensured development of high producing breeds, however, the thermotolerance ability of animals has been largely overlooked. In the past decade, the ill effects of climate change have made it pertinent to rethink the selection strategies to opt for climate resilient breeds, to ensure optimum production and reproduction. This has led to renewed interest in evaluation of the impacts of heat stress on cows and the underlying mechanisms that results in their acclimatization and adaptation to varied thermal ambience. The understanding of heat stress and associated responses at various level of animal is crucial to device amelioration strategies to secure optimum production and welfare of cows. With this review, an effort has been made to provide an overview on temperature humidity index as an important indicator of heat stress, general effect of heat stress in dairy cows, and impact of heat stress and subsequent response at physiological, haematological, molecular and genetic level of dairy cows.

Differentially expressed microRNAs in biochemically characterized FrieswalTM crossbred bull semen

In addition to the transmission of paternal genome, spermatozoa also carry coding as well as noncoding microRNAs (miRNAs) into the female oocyte during the process of biological fertilization. Based on RNA deep sequencing, a total 28 number of differentially expressed miRNAs were cataloged in categorized Frieswal^TM crossbred (Holstein Friesian X Sahiwal) bull semen on the basis of conception rate (CR) in field progeny testing program. Validation of selected miRNAs viz. bta-mir-182, bta-let-7b, bta-mir-34c and bta-mir-20a revealed that, superior bull semen having comparatively (p < .05) lower level of all the miRNAs in contrast to inferior bull semen. Additionally, it was illustrated that, bta-mir-20a and bta-mir-34c miRNAs are negatively (p < .01) correlated with seminal plasma catalase (CAT) activity and glutathione peroxidase (GPx) level. Interactome studies identified that bta-mir-140, bta-mir-342, bta-mir-1306 and bta-mir-217 can target few of the important solute carrier (SLC) proteins viz. SLC30A3, SLC39A9, SLC31A1 and SLC38A2, respectively. Interestingly, it was noticed that all the SLCs were significantly (p < .05) expressed at higher level in superior quality bull semen and they are negatively correlated (p < .01) with their corresponding miRNAs as mentioned. This study may reflect the role of miRNAs in regulating few of the candidate genes and thus may influence the bull semen quality traits.

Expression Profile of miRNA from High, Middle, and Low Stress-Responding Sheep during Bacterial Endotoxin Challenge

Animals respond to stress by activating a wide array of physiological and behavioral responses that are collectively referred to as the stress response. MicroRNAs (miRNAs) are small, noncoding RNAs that play key roles in the regulation of homeostasis. There are many reports demonstrating examples of stress-induced miRNA expression profiles. The aim of this study was to determine the circulatory miRNA profile of variable stress-responding lambs (n = 112) categorized based on their cortisol levels as high (HSR, 336.2 ± 27.9 nmol/L), middle (MSR, 147.3 ±9.5 nmol/L), and low (LSR, 32.1 ± 10.4 nmol/L) stress responders post-LPS challenge (400 ng/kg iv). Blood was collected from the jugular vein at 0 (T0) and 4 h (T4) post-LPS challenge, and miRNAs were isolated from four animals from each group. An array of 84 miRNAs and 6 individual miRNAs were evaluated using qPCR. Among 90 miRNAs, there were 48 differentially expressed (DE) miRNAs (log fold change (FC) > 2 < log FC) in the HSR group, 46 in the MSR group, and 49 in the LSR group compared with T0 (control) samples. In the HSR group, three miRNAs, miR-485-5p, miR-1193-5p, and miR-3957-5p were significantly (p < 0.05) upregulated, while seven miRNAs, miR-376b-3p, miR-376c-3p, miR-411b-5p, miR-376a-3p, miR-376b-3p, miR-376c-3p, and miR-381-3p, were downregulated (p < 0.05) as compared to the LSR and MSR groups. Functional analysis of DE miRNAs revealed their roles in Ras and MAPK signaling, cytokine signaling, the adaptive immune system, and transcription pathways in the HSR phenotype, implicating a hyper-induced acute-phase response. In contrast, in the LSR group, enriched pathways included glucagon signaling metabolic regulation, the transportation of amino acids and ions, and the integration of energy metabolism. Taken together, these results indicate variation in the acute-phase response to an immune stress challenge, and these miRNAs are implicated in regulating responses within cortisol-based phenotypes.

Characterization of thermo-physiological, hematological, and molecular changes in response to seasonal variations in two tropically adapted native cattle breeds of Bos indicus lineage in hot arid ambience of Thar Desert

The selection of climate resilient animal is necessary to secure the future of sustainable animal production. The present investigation therefore was an effort to unravel answers to the adaptation at physiological, hematological, and molecular levels in cows of hot arid region that helps them to survive harsh environment, to continue production and reproduction. This investigation was carried out in indicine cows over a period of one year, encompassing four seasons, wherein physiological data of 50 animals, hematological data of 15 animals, and gene expression profile of 5 animals from each of Sahiwal and Kankrej breeds per season was generated. In total, 5600 physiological observations, 1344 hematological observations, and 480 molecular samples were processed. The meteorological data revealed a high diurnal variation of temperature across seasons, with THI exceeding 80 during the months of summer and hot-humid seasons, indicating significant heat stress (HS). The physiological parameters showed an increasing trend with the incremental THI, with significantly (p < 0.05) higher values of rectal temperature (RT), respiration rate (RR), pulse rate (PR), and body surface temperature (BST) at ventral (VT), lateral (LT), dorsal (DT), and frontal (FT), in both breeds recorded during HS. The hematological pictures also revealed significant (p < 0.05) seasonal perturbations in erythrocytic and leucocytic parameters. Moreover, the molecular response was driven by a significant (p < 0.05) upregulation of all the key HSPs, HSP70, HSP90, HSP60, and HSP40, except HSP27 during the hotter months of summer and hot-humid seasons. The expression of HSF1, an important transcriptional regulator of  HSP70 was also significantly (p < 0.05) upregulated during summer season in both breeds. All the molecular chaperones revealed a significant upregulation during the summer season, followed by a decreasing trend by hot-humid season. The study indicated a well-developed thermotolerance mechanism in animals of both breeds, with Kankrej cows exhibiting better thermotolerance compared to Sahiwal cows.

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

In Silico Investigation of Conserved miRNAs and Their Targets From the Expressed Sequence Tags in Neospora Caninum Genome

Neospora caninum is a protozoan parasite, the etiologic agent of Neosporosis—a common cause of abortion in cattle worldwide. Herd level prevalence of Neosporosis could be as high as 90%. However, there is no approved treatment and vaccines available for Neosporosis. MicroRNA (miRNA) based prophylaxis and therapeutics could be options for Neosporosis in cattle and other animals. The current study aimed to investigate the genome of Neospora caninum to identify and characterize the conserved miRNAs through Expressed Sequence Tags (ESTs) dependent homology search. A total of 1,041 mature miRNAs of reference organisms were employed against 336 non-redundant ESTs available in the genome of Neospora caninum. The study predicted one putative miRNA “nca-miR-9388-5p” of 19 nucleotides with MFEI value -1.51 kcal/mol and (A + U) content% 72.94% corresponding with its pre-miRNA. A comprehensive search for specific gene targets was performed and discovered 16 potential genes associated with different protozoal physiological functions. Significantly, the gene “Protein phosphatase” was found responsible for the virulence of Neospora caninum. The other genes were accounted for gene expression, vesicular transport, cell signaling, cell proliferation, DNA repair mechanism, and different developmental stages of the protozoon. Therefore, this study finding will provide pivotal information to future aspirants upon Bovine Neosporosis. It will also serve as the baseline information for further studies of the bioinformatics approach to identify other protozoal miRNAs.

The Role of microRNAs in the Mammary Gland Development, Health, and Function of Cattle, Goats, and Sheep

Milk is an integral and therefore complex structural element of mammalian nutrition. Therefore, it is simple to conclude that lactation, the process of producing milk, is as complex as the mammary gland, the organ responsible for this biochemical activity. Nutrition, genetics, epigenetics, disease pathogens, climatic conditions, and other environmental variables all impact breast productivity. In the last decade, the number of studies devoted to epigenetics has increased dramatically. Reports are increasingly describing the direct participation of microRNAs (miRNAs), small noncoding RNAs that regulate gene expression post-transcriptionally, in the regulation of mammary gland development and function. This paper presents a summary of the current state of knowledge about the roles of miRNAs in mammary gland development, health, and functions, particularly during lactation. The significance of miRNAs in signaling pathways, cellular proliferation, and the lipid metabolism in agricultural ruminants, which are crucial in light of their role in the nutrition of humans as consumers of dairy products, is discussed.

Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr

Whole genome sequencing of bovine breeds has allowed identification of genetic variants in milk protein genes. However, functional repercussion of such variants at a molecular level has seldom been investigated. Here, the results of a multistep Bioinformatic analysis for functional characterization of recently identified genetic variants in Brazilian Gyr and Guzerat breeds is described, including predicted effects on the following: (i) evolutionary conserved nucleotide positions/regions; (ii) protein function, stability, and interactions; (iii) splicing, branching, and miRNA binding sites; (iv) promoters and transcription factor binding sites; and (v) collocation with QTL. Seventy-one genetic variants were identified in the caseins (CSN1S1, CSN2, CSN1S2, and CSN3), LALBA, LGB, and LTF genes. Eleven potentially regulatory variants and two missense mutations were identified. LALBA Ile60Val was predicted to affect protein stability and flexibility, by reducing the number the disulfide bonds established. LTF Thr546Asn is predicted to generate steric clashes, which could mildly affect iron coordination. In addition, LALBA Ile60Val and LTF Thr546Asn affect exonic splicing enhancers and silencers. Consequently, both mutations have the potential of affecting immune response at individual level, not only in the mammary gland. Although laborious, this multistep procedure for classifying variants allowed the identification of potentially functional variants for milk protein genes.

Behavioural, physiological, neuro-endocrine and molecular responses of cattle against heat stress: an updated review

The negative impact of heat stress on cattle growth, development, reproduction and production has been quite alarming across the world. Climate change elevates earth surface temperature which exacerbates the wrath of heat stress on cattle. Moreover, cattle in tropical and sub-tropical countries are most commonly affected by the menace of heat stress which severely wane their production and productivity. In general, cattle exhibit various thermoregulatory responses such as behavioural, physiological, neuro-endocrine and molecular responses to counteract the terrible effects of heat stress. Amongst the aforementioned thermoregulatory responses, behavioural, physiological and neuro-endocrine responses are regarded as most conventional and expeditious responses shown by cattle against heat stress. Furthermore, molecular responses serve as the major adaptive response to attenuate the harmful effects of heat stress. Therefore, present review highlights the significance of behavioural, physiological, neuro-endocrine and molecular responses which act synergistically to combat the deleterious effects of heat stress thereby confer thermo-tolerance in cattle.

Cellular and Molecular Insights Into the Etiology of Subfertility/Infertility in Crossbred Bulls (Bos taurus × Bos indicus): A Review

Crossbreeding of indigenous cattle (Bos indicus) with improved (Bos taurus) breeds gained momentum and economic relevance in several countries to increase milk production. While production performance of the crossbred offspring is high due to hybrid vigor, they suffer from a high incidence of reproductive problems. Specifically, the crossbred males suffer from serious forms of subfertility/infertility, which can have a significant effect because semen from a single male is used to breed several thousand females. During the last two decades, attempts have been made to understand the probable reasons for infertility in crossbred bulls. Published evidence indicates that testicular cytology indices, hormonal concentrations, sperm phenotypic characteristics and seminal plasma composition were altered in crossbred compared to purebred males. A few recent studies compared crossbred bull semen with purebred bull semen using genomics, transcriptomics, proteomics and metabolomics; molecules potentially associated with subfertility/infertility in crossbred bulls were identified. Nevertheless, the precise reason behind the poor quality of semen and high incidence of sub-fertility/infertility in crossbred bulls are not yet well defined. To identify the underlying etiology for infertility in crossbred bulls, a thorough understanding of the magnitude of the problem and an overview of the prior art is needed; however, such systematically reviewed information is not available. Therefore, the primary focus of this review is to compile and analyze earlier findings on crossbred bull fertility/infertility. In addition, the differences between purebred and crossbred males in terms of testicular composition, sperm phenotypic characteristics, molecular composition, environmental influence and other details are described; future prospects for research on crossbred males are also outlined.

Comparative CpG methylation kinetic patterns of cis-regulatory regions of heat stress-related genes in Sahiwal and Frieswal cattle upon persistent heat stress

The kinetic patterns of CpG methylation of the cis-regulatory region of heat stress-related genes on exposed to heat stress (at 42 °C) between the Sahiwal and Frieswal cattle was compared in the present study. Using an in vitro whole blood culture model, cells were continuously exposed to heat stress (at 42 °C) for 6 h. Methylation levels of five genes, viz., GPX1, HSP70, HSP90, c-FOS, and JUN were estimated by SyberGreen-based quantitative methylation-specific PCR (qMSP) assay. CpG methylation kinetics at different time points of heat stress (0.5, 1, 2, 4, 6 h) were analyzed using mixed ANOVA. The initial methylation level, estimated at 37 °C, of HSP70 was significantly high in the Sahiwal breed. A significant (p<0.001) time-dependent hypomethylation of an antioxidant gene (GPX1) CpG islands was detected at the acute phase of the stress. Heat shock protein gene (HSP70) showed a similar CpG methylation kinetics where the hypomethylation was prominent from 1 h and persisted up to 4 h. The heat stress responses of both Sahiwal and Frieswal cattle were identical as there was no distinctiveness in the methylation kinetics of CpG islands of studied genes. The acclimatization of Frieswal cattle-a breed developed in India over the years to the tropical climatic conditions, maybe one of the reasons for this similarity. Thus, the present study results could pave a path to understand the molecular mechanism of heat stress and adaptation of indigenous and crossbred cattle populations to the changing scenario in tropical climate conditions.

Heat shock during in vitro maturation of bovine oocytes disturbs bta-miR-19b and DROSHA transcripts abundance after in vitro fertilization

While microRNAs (miRNAs) are a class of non-coding RNAs important for embryo development, the relationship between them and heat stress during oocyte maturation has not yet been established. This study investigated the effect of heat shock during in vitro maturation (IVM) on the abundance of bta-miR-20a, -27b, -103, -21-5p, -19b, -1246 miRNAs and DROSHA and DICER1 mRNAs, previously reported for being involved in oocyte maturation, response to heat stress and miRNA biogenesis. Oocytes were exposed for 12h to heat shock during IVM, fertilized in vitro and the presumptive zygotes cultured for eight days. The relative quantification of miRNAs and mRNAs was performed by real-time PCR in vitro-matured oocytes and 8-cell stage embryos. Progression of meiosis, embryonic development and apoptotic indices was also evaluated. Heat shock compromised (p < .05) oocyte nuclear maturation, cleavage and embryo development, with a higher (p < .05) embryonic apoptotic index than the control group. The abundance of bta-miR-19b increased (p < .05) whereas the abundance of DROSHA transcripts decreased (p < .05) in embryos derived from heat-shocked oocytes. In conclusion, heat shock during IVM influences the abundance of bta-miR-19b and DROSHA in pre-implantation embryos, indicating a persistent effect of heat shock that can be associated with impaired embryo development.

Novel and known miRNAs in zebu (Tharparkar) and crossbred (Karan-Fries) cattle under heat stress

MicroRNAs (miRNAs) are small single-stranded non-coding RNAs that act as the master regulator of animal growth and development. RNA-RNA interaction is an important mechanism of gene regulation during biotic and abiotic stress. Heat stress (HS) is one of the most important abiotic factors which affect the growth, milk yield and reproductive health of the dairy animals. In the present investigation, we identified 387 known and 77 novel miRNAs from Tharparkar (TH) and Karan Fries (KF) cattle under HS condition. Family distribution analysis showed the identified miRNAs belong to more than 15 different families in which miR-2284 was the most abundant. We identified 42,350 targets for the known miRNAs reported in cattle. Pathway analysis of the identified targets showed most of the target genes were involved in cancer, mitogen-activated protein kinase (MAPK) signaling, calcium signaling, Ras signaling, and cAMP signaling pathways. Differential gene expression showed more than 344 miRNAs changed their expression significantly between control and HS condition. Heat map was generated for the top 20 most up and downregulated miRNAs. Ten miRNAs were validated using qRT-PCR to be heat responsive, based on read count value and differential gene expression. These novel miRNAs are new addition to the miRNA database of cattle. This study provides an overview of miRNA profile and their interaction with the target genes which leads to further understanding in deciphering the thermotolerance mechanism in cattle.

Nutrigenomic analyses reveal miRNAs and mRNAs affected by feed restriction in the mammary gland of midlactation dairy cows

The objective of this study was to investigate the effects of feed restriction on mammary miRNAs and coding gene expression in midlactation cows. Five Holstein cows and 6 Montbéliarde cows underwent 6 days of feed restriction, during which feed allowance was reduced to meet 50% of their net energy for lactation requirements. Mammary biopsies were performed before and at the end of the restriction period. Mammary miRNA and mRNA analyses were performed using high-throughput sequencing and microarray analyses, respectively. Feed restriction induced a negative energy balance and decreased milk production and fat and protein yields in both breeds. Feed restriction modified the expression of 27 miRNAs and 374 mRNAs in mammary glands from Holstein cows, whereas no significant miRNA change was observed in Montbéliarde cows. Among the 27 differentially expressed miRNAs, 8 miRNAs were associated with dairy QTL. Analysis of target genes indicate that the 8 most abundantly expressed miRNAs control transcripts related to lipid metabolism, mammary remodeling and stress response. A comparison between the mRNAs targeted by the 8 most strongly expressed miRNAs and 374 differentially expressed mRNAs identified 59 mRNAs in common. The bioinformatic analyses of these 59 mRNAs revealed their implication in lipid metabolism and endothelial cell proliferation. These effects of feed restriction on mammary miRNAs and mRNAs observed in Holstein cows suggest a potential role of miRNAs in mammary structure and lipid biosynthesis that could explain changes in milk production and composition.

Differential expression of miRNAs and related mRNAs during heat stress in buffalo heifers

The present experiment was aimed to study differential expression of miRNAs and related mRNAs during heat stress (HS) in buffalo heifers. Twelve Murrah buffalo heifers aged between 1.5 and 2.0 years, weighting between 250 and 300 Kg were randomly assigned into two equal groups. The animals were kept in the psychrometric chamber under Thermo-neutral (TN; THI = 72) and HS (THI = 87-90) conditions for 6 h every day between 1000 and 1600 h for 21 days. The blood sampling was done at 1500 h on 15th day of the experiment and physiological parameters viz. pulse rate (PR), respiratory rate (RR) and rectal temperature (RT) were recorded at 1500 h on day -5, -3, -1, 0, +1, +3, +5 with respect to blood sampling. PBMCs were used for extraction of miRNAs and total RNA; and first strand cDNA was synthesized. qPCR was performed for relative gene expression studies. Physiological, hematological (erythrocytic indices), biochemical (triglycerides, urea, ALT, AST, LDH), redox (SOD, ROS) and endocrine parameters (T₄) altered significantly (P < 0.05) during HS as compared to TN. Out of eight targeted miRNAs only four were expressed in buffalo heifers. The relative expression of bta-mir-142, bta-mir-1248 and bta-mir-2332 was significantly (P < 0.05) up-regulated whereas expression of bta-mir-2478 was significantly (P < 0.05) down-regulated during HS as compared to TN. The relative expression of the predicted target genes i.e. HSF1, HSP60, HSP70, HSPA8 and HSP90 were significantly (P < 0.05) up-regulated whereas HSF4 expression was significantly (P < 0.05) down-regulated during HS as compared to TN. It can be concluded that a THI of 87-90 could lead to a moderate HS in buffalo heifers. Differential expression studies of miRNAs and related mRNAs in present study deciphers the role of miRNAs in the heat tolerance in buffalo heifers.

Comparative miRNA signatures among Sahiwal and Frieswal cattle breeds during summer stress

MicroRNAs (miRNAs) are known to take part in different biological mechanisms, including biotic as well as abiotic cellular stresses. The present investigation was aimed to identify comparative expression profile of differentially expressed miRNAs among Sahiwal (Bos indicus) and Frieswal (Bos indicus × Bos taurus) cattle breeds during summer stress. Stress responses in animals were characterized by recording various physiological parameters, biochemical assays and expression profiling of heat shock protein 70 (Hsp70) during elevated environmental temperature. Ion Torrent-based deep sequencing as well as CLC-genomic analysis identified 322 and 420 Bos taurus annotated miRNAs among Sahiwal and Frieswal, respectively. A total 69 common miRNAs were identified to be differentially expressed during summer among the breeds. Out of the 69, a total 14 differentially expressed miRNAs viz. bta-mir 6536-2, bta-mir-2898, bta-mir-let-7b, bta-mir-425, bta-mir-2332, bta-mir-2478, bta-mir-150, bta-mir142, bta-mir-16a, bta-mir-2311, bta-mir-1839, bta-mir-1248-1, bta-mir-103-2 and bta-mir-181b were randomly selected for qRT-PCR-based validation. bta-mir-2898, bta-mir-6536-1, bta-mir-let-7b, bta-mir-2478, bta-mir-150, bta-mir-16a, bta-mir-2311, bta-mir-1032-b and bta-mir-181-b were significantly (p < 0.01) upregulated during summer among Frieswal in comparison to Sahiwal while, bta-mir 6536-2, bta-mir-2332, bta-mir142, bta-mir-1839 and bta-mir-1248-1 was significantly (p < 0.01) expressed at higher level in Sahiwal in contrast to Frieswal correlation coefficient analysis revealed that bta-mir(s)-150, 16a and 181b are negatively correlated (p < 0.05) with Hsp70 expression. Thus, this study identified that miRNA expression during summer stress can vary between the breeds which may reflect their differential post-transcriptional regulation.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02608-4.

Potential role of specific microRNAs in the regulation of thermal stress response in livestock

Thermal stress is known to have harmful effects on livestock productivity and can cause livestock enterprises considerable financial loss. These effects may be aggravated by climate change. Stress responses to nonspecific systemic actions lead to perturbation of molecular pathways in the organism. The molecular response is regulated in a dynamic and synchronized manner that assurances robustness and flexibility for the restoration of functional and structural homeostasis in stressed cells and tissues. MicroRNAs (miRNAs) are micro molecules of small non-coding RNA that control gene expression at the post-transcriptional level. Recently, various studies have discovered precise types of miRNA that regulate cellular machinery and homeostasis under various types of stress, suggesting a significant role of miRNA in thermal stress responses in animals. The miRNAs revealed in this paper could serve as promising candidates and biomarkers for heat stress and could be used as potential pharmacological targets for mitigating the consequences of thermal stress. Stress miRNA pathways may be associated with thermal stress, which offers some potential approaches to combat the negative impacts of thermal stress in livestock. The review provides new data that can assist the elucidation of the miRNA mechanisms that mediate animals' responses to thermal stress.

Thermoregulatory responses in riverine buffaloes against heat stress: An updated review

High heat and humidity stress have been a perpetual perilous for the buffalo's production and productivity in tropics and subtropics including India. Productive potential of livestock's species including buffaloes is maximum with in thermo-neutral zone (TNZ) and if ambient temperature exceeds TNZ and upper critical temperature expose livestock's to heat stress conditions. For decades, heat stress has been the prime factor to plummet buffalo's growth, development, reproduction and production in tropics and subtropics including India. In general, buffaloes are homeotherms and known as temperature regulators as they resist the variations in ambient temperatures. Generally, buffaloes like other livestock's display amalgamation of thermoregulatory responses to withstand the changes occurred in their micro and macro environment. These thermoregulatory responses are behavioural, physiological, neuro-endocrine and molecular responses acting synergistically to counteract the deleterious effects of heat stress. Amidst all responses, molecular responses play major role to confer thermo-tolerance through expression of highly conserved family of proteins known as heat shock proteins (HSPs). Despite of these thermoregulatory responses, heat stress prodigiously muddles buffalo's production and productivity. The present review highlights the thermoregulatory responses manifested by riverine buffaloes against heat stress.

Significance of molecular chaperones and micro RNAs in acquisition of thermo-tolerance in dairy cattle

Ambient temperature is considered as the major abiotic factor which regulates body physiological mechanisms of all living creatures across the globe. Variation in ambient temperature which emulates thermoneutral zone culminates in heat stress. Heat stress has been emerged as major ultimatum to livestock's growth, development, production and reproduction across the world. Livestock's responds to the heat stress via different mechanisms such as behavioral, physiological, biochemical, endocrine and molecular mechanisms. Amongst the aforementioned mechanisms, molecular mechanism plays crucial role to achieve thermo-tolerance via expression of highly conserved family of proteins known as heat shock proteins (HSPs) across livestock species. HSPs serve as molecular chaperones to ameliorate the menace of heat stress in domestic species. In addition, microRNAs are small non-coding RNA which down regulates post-transcriptional gene expression by targeting various HSPs to regulate the thermoregulatory responses in livestock species. Despite of thermal adaptation mechanisms, heat stress breaches animal body homeostasis thereby depresses their production and productivity. Therefore, veterinary researches have been targeting to explore different repertoire of HSPs and microRNAs expression to counteract the rigors of heat stress thereby confer thermo-tolerance in livestock species. The present review highlights the significance of molecular chaperones and microRNAs in the acquisition of thermo-tolerance in dairy cattle.

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

Background

Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions.

Results

Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C).

Conclusions

We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.

Heat stress modulates differential response in skin fibroblast cells of native cattle (Bos indicus) and riverine buffaloes (Bubalus bubalis)

Heat stress in hot climates is a major cause that negatively affects dairy animals, leading to substantial economic loss. The present study was aimed to analyze the effect of heat stress on cellular and molecular levels in dermal fibroblast of cattle and buffaloes. Primary fibroblast culture was established using ear pinna tissue samples of cattle (Bos indicus) and riverine buffaloes (Bubalus Bubalis). The cells were exposed to thermal stress at 42°C for 1 h and subsequently allowed to recover and harvest at 37°C at different time points (0, 2, 4, 8, 16, and 24 h) along with control samples. Different cellular parameters viz., apoptosis, proliferation, mitochondrial membrane potential (ΔΨm), oxidative stress, along with expression pattern of heat responsive genes and miRNAs were determined. Cell viability and proliferation rate of heat-stressed fibroblasts decreased significantly (P < 0.05) albeit to a different extent in both species. The cell cytotoxicity, apoptosis, production of reactive oxygen species, and ΔΨm increased more significantly (P < 0.01) in heat stressed fibroblasts of buffalo than cattle. The pattern of heat shock proteins, inflammation/immune genes, and heat responsive miRNA showed differences in induction of their expression level in buffalo and native cattle fibroblasts. Conclusively, finding indicates that heat stress induces more profound impact on buffalo fibroblasts than native cattle fibroblasts. The differential response of cellular parameters, HSP genes, and miRNA expression could be due to better adaptive capacity of skin fibroblast of Bos indicus cattle in comparison with riverine buffaloes.

Heat stress-induced alterations in the expression of genes associated with gonadal integrity of the teleost Puntius sophore

Temperature plays an important role on reproductive physiology of vertebrates including mammals, fish, and birds. It has varying effects on fish reproduction depending on the species; higher temperatures favor the spring-spawning species, while lower temperatures stimulate reproduction in autumn spawners. To evaluate the impact of high temperature on the reproductive physiology of minnow Puntius sophore, we carried out expression analysis of selected genes associated with gamete quality (hsp60, hsp70, hsp90, hsf1, vtg), pleuripotency (sox2, oct4, nanog), and sex determination (dmrt1) in gonads (ovary and testis) of P. sophore, heat stressed for different time periods (36 °C/7 days or 60 days) using real-time quantitative polymerase chain reaction (RT-qPCR). Expression of most of the hsp, vtg, and pleuripotency marker genes sox-2, oct-4, and nanog genes was downregulated in both ovary and testis of heat-stressed fish. The expression of dmrt-1 was upregulated in testis but downregulated in ovary of the heat-stressed fish which could be a male favoring effect of high temperature in P. sophore. This study suggests that the reproductive physiology and health of the nutrient dense P. sophore would be negatively affected by high temperature stress.

Genome-wide association for milk production traits and somatic cell score in different lactation stages of Ayrshire, Holstein, and Jersey dairy cattle

We performed genome-wide association analyses for milk, fat, and protein yields and somatic cell score based on lactation stages in the first 3 parities of Canadian Ayrshire, Holstein, and Jersey cattle. The genome-wide association analyses were performed considering 3 different lactation stages for each trait and parity: from 5 to 95, from 96 to 215, and from 216 to 305 d in milk. Effects of single nucleotide polymorphisms (SNP) for each lactation stage, trait, parity, and breed were estimated by back-solving the direct breeding values estimated using the genomic best linear unbiased predictor and single-trait random regression test-day models containing only the fixed population average curve and the random genomic curves. To identify important genomic regions related to the analyzed lactation stages, traits, parities and breeds, moving windows (SNP-by-SNP) of 20 adjacent SNP explaining more than 0.30% of total genetic variance were selected for further analyses of candidate genes. A lower number of genomic windows with a relatively higher proportion of the explained genetic variance was found in the Holstein breed compared with the Ayrshire and Jersey breeds. Genomic regions associated with the analyzed traits were located on 12, 8, and 15 chromosomes for the Ayrshire, Holstein, and Jersey breeds, respectively. Especially for the Holstein breed, many of the identified candidate genes supported previous reports in the literature. However, well-known genes with major effects on milk production traits (e.g., diacylglycerol O-acyltransferase 1) showed contrasting results among lactation stages, traits, and parities of different breeds. Therefore, our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the analyzed traits across breeds, parities, and lactation stages. Further functional studies are needed to validate our findings in independent populations.

Rapid identification and interpretation of gene-environment associations using the new R.SamBada landscape genomics pipeline

samβada is a genome–environment association software, designed to search for signatures of local adaptation. However, pre‐ and postprocessing of data can be labour‐intensive, preventing wider uptake of the method. We have now developed R.SamBada, an r‐package providing a pipeline for landscape genomic analysis based on samβada, spanning from the retrieval of environmental conditions at sampling locations to gene annotation using the Ensembl genome browser. As a result, R.SamBada standardizes the landscape genomics pipeline and eases the search for candidate genes of local adaptation, enhancing reproducibility of landscape genomic studies. The efficiency and power of the pipeline is illustrated using two examples: sheep populations from Morocco with no evident population structure and Lidia cattle from Spain displaying population substructuring. In both cases, R.SamBada enabled rapid identification and interpretation of candidate genes, which are further discussed in the light of local adaptation. The package is available in the r CRAN package repository and on GitHub (github.com/SolangeD/R.SamBada).

Tropical milk production systems and milk quality: a review

We reviewed information on dairy cattle production systems in the tropics, the factors involved, and their influence on milk composition. Genetic factors had greater influence on milk production; specialized breeds produced more milk, and there was an inverse relation between the content of fat, protein, total solids, and the amount of milk produced. Season was related to the availability of forage, and the type of grazing system. Greater pasture area increased individual production, while a greater supply of feed concentrate did not increase milk production. The number of calvings positively affected milk production through the fifth calving, with subsequent declines in production. Milk production increased to a maximum and then declined as lactation progressed. Specialized systems had higher production and better hygienic milk quality; milking and container equipment are critical for maintaining milk sanitary quality. Factor interaction is highly complex, preventing the generation of specific recommendations and general principles applicable to the specific conditions for each system.

Changes in morphology and miRNAs expression in small intestines of Shaoxing ducks in response to high temperature

During summer days the extreme heat may cause damage to the integrity of animal intestinal barrier. Little information is available concerning morphological changes in the duck intestines in response to high temperature. And the molecular mechanisms underlying the pathogenesis of high temperature-induced intestinal injury remain undefined. MicroRNAs (miRNAs) are known to play key roles in post-transcriptional regulation of gene expression that influences various biological processes. The purpose of this study was to explore the changes in morphology and miRNA expression profiles of the three intestinal segments (duodenum, jejunum and ileum) of ducks in response to high temperature. Sixty female Shaoxing ducks (Anas platyrhynchos), 60 days old, were allocated in two groups, including control ducks kept at 25 °C, and ducks subjected to high ambient temperatures of 30-40 °C for 15 successive days, which mimicked the diurnal temperature variations experienced in hot seasons. Three ducks from each group were executed at the end of feeding experiment, and the samples of three intestinal segments were collected for morphological examination and Illumina deep sequencing analyses. Histopathological examination of the intestinal mucous membrane was performed with HE staining method. The results demonstrated that varying degrees of damage to each intestinal segment were found in heat-treated ducks, and there were more severe injuries in duodenum and jejunum than those in ileum. Illumina high-throughput sequencing and bioinformatic methods were employed in this study to identify the miRNA expression profile of three different intestinal tissues in control and heat-treated ducks. A total of 75,981,636, 88,345,563 and 100,179,422 raw reads were obtained from duodenum, jejunum and ileum, respectively, from which 74,797,633 clean reads in duodenal libraries, 86,406,445 clean reads in jejunal libraries, and 98,518,858 lean reads in ileal libraries were derived after quality control, respectively. And a total of 276 known and 182 novel miRNAs were identified in the three intestinal segments of ducks under control and heat-treated conditions. By comparing the same tissues in different conditions, 16, 18 and 15 miRNAs were found to be significantly differentially expressed between control and heat-treated ducks in duodenum, jejunum and ileum, respectively, of which 1 miRNA was expressed in both the duodenum and jejunum, 2 miRNAs were expressed in both the duodenum and ileum, and 3 miRNAs were found to be expressed in both the jejunum and ileum. In addition, two differentially expressed miRNAs in each comparison were randomly selected and validated by quantitative qRT-PCR. Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that the differentially expressed miRNAs may be involved in the high temperature-induced intestinal injury in ducks. Our work provides the comprehensive miRNA expression profiles of small intestines in the normal and heat-treated ducks. These findings suggest the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the high temperature-induced changes in the duck small intestine.

Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data

Heat stress has a detrimental effect on the physiological and production performance of buffaloes. Elucidating the underlying mechanisms of heat stress is challenging, therefore identifying candidate genes is urgent and necessary. We evaluated the response of buffaloes (n = 30) to heat stress using the physiological parameters, ELISA indexes, and hematological parameters. We then performed mRNA and microRNA (miRNA) expression profiles analysis between heat tolerant (HT, n = 4) and non-heat tolerant (NHT, n = 4) buffaloes, as well as the specific modules, significant genes, and miRNAs related to the heat tolerance identified using the weighted gene co-expression network analysis (WGCNA). The results indicated that the buffaloes in HT had a significantly lower rectal temperature (RT) and respiratory rate (RR) and displayed a higher plasma heat shock protein (HSP70 and HSP90) and cortisol (COR) levels than those of NHT buffaloes. Differentially expressed analysis revealed a total of 753 differentially expressed genes (DEGs) and 16 differentially expressed miRNAs (DEmiRNAs) were identified between HT and NHT. Using the WGCNA analysis, these DEGs assigned into 5 modules, 4 of which were significantly correlation with the heat stress indexes. Interestingly, 158 DEGs associated with heat tolerance in the turquoise module were identified, 35 of which were found within the protein-protein interaction network. Several hub genes (IL18RAP, IL6R, CCR1, PPBP, IL1B, and IL1R1) were identified that significantly enriched in the Cytokine-cytokine receptor interaction. The findings may help further elucidate the underlying mechanisms of heat tolerance in buffaloes.

MicroRNA-155 Promotes Heat Stress-Induced Inflammation via Targeting Liver X Receptor α in Microglia

Background: The neuroinflammatory responses of microglial cells play an important role in the process of brain dysfunction caused by heat stroke. MicroRNAs are reportedly involved in a complex signaling network and have been identified as neuroinflammatory regulators. In this study, we determined the biological roles of microRNA-155 in the inflammatory responses in heat-stressed microglia and explored the underlying mechanisms.

Methods: MicroRNA-155 mimic and inhibitor were used to separately upregulate or downregulate microRNA-155 expression. The activation state of BV-2 microglial cells (BV-2 cells) was assessed via immunoreactions using the microglial marker CD11b and CD68. Levels of induced interleukin-1β (IL-1β), interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) were measured using real-time reverse transcription polymerase chain reaction (RT-PCR) and enzyme linked immunosorbent assays (ELISAs). The activation of nuclear factor kappa B (NF-κB) signaling proteins was evaluated by Western blotting for inhibitory kappa B alpha (IκBα) and NF-κB p65 phosphorylation and indirect immunofluorescence analysis using a p65 phosphorylation antibody. A luciferase reporter assay was used to verify liver X receptor α (LXRα) as a target gene of microRNA-155.

Results: Heat stress significantly induced IL-1β, IL-6, and TNF-α release and increased the expression of CD11b and CD68. In addition, IκBα and NF-κB p65 phosphorylation were dramatically increased by heat stress, and microRNA-155 expression was also elevated. High expression of microRNA-155 in heat-stressed microglial cells was inversely correlated with LXRα expression. We then determined the role of microRNA-155 in the heat stress-induced inflammatory responses. The results revealed that by targeting LXRα, microRNA-155 enhanced NF-κB signaling activation and facilitated immune inflammation in heat stress-treated BV-2 cells.

Conclusion: MicroRNA-155 promotes heat stress-induced inflammatory responses in microglia. The underlying mechanisms may include facilitating inflammatory factors expression by increasing NF-κB pathway activation via targeting LXRα.

Characterization of miRNA profiles in the mammary tissue of dairy cattle in response to heat stress

Background

MicroRNAs (miRNAs) are a class of small noncoding RNAs that play important roles in the regulation of gene expression. However, the role of miRNAs in bovine mammary gland responses to heat stress is not well understood.

Results

In the present study, we performed a deep RNA sequencing analysis to identify miRNAs associated with the heat stress potential of the bovine mammary gland. We identified 27 miRNAs that were differentially expressed significantly between the mammary tissue of Holstein cattle heat stress and normal conditions. Twenty miRNAs had higher expression in the mammary tissue of heat-stressed Holstein cattle. The seven highest differentially expressed candidate miRNAs (bta-miR-21-5p, bta-miR-99a-5p, bta-miR-146b, bta-miR-145, bta-miR-2285 t, bta-miR-133a, and bta-miR-29c) identified by deep RNA sequencing were additionally evaluated by stem-loop qPCR. Enrichment analyses for targeted genes revealed that the major differences between miRNAs expression in the mammary gland of heat-stressed versus control were associated with the regulation of Wnt, TGF-β, MAPK, Notch, and JAK-STAT.

Conclusions

These data indicated that the differentially expressed miRNAs identified in this study may act as dominant regulators during heat stress. We might reduce heat stress damage of Holstein cows by up-regulating or down-regulating these differentially expressed miRNAs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5298-1) contains supplementary material, which is available to authorized users.

Differential expression of miRNAs in milk exosomes of cows subjected to group relocation

This study examined microRNA (miRNAs) expression and regulatory patterns from milk exosomes of cows experienced group relocation, a common husbandry practice during the lactation period and used as a spontaneous model of stress. Total RNA from milk exosome samples was collected from 3 cows that showed an increased milk cortisol (HRC) after relocation (T2 vs T1) and 3 cows that did not show cortisol increase (LRC). A total of 69 known miRNAs were identified. Thirteen miRNAs were consistently down-regulated at T2 in comparison to T1, such as miR-2904-1, miR-142, miR-2284x and miR-30b-3p. Only two miRNAs, miR-2284z and miR-146a were significantly different between LRC and HRC group. Functional enrichment analyses highlighted that glucocorticoid receptor signaling and neurotrophic factor mediated TRK receptor signaling were among the biological pathways affected by differentially expressed miRNA target genes. Mir-135a-5p and miR-320a were involved in both biological pathways. miR-142-5p, miR-142-3p, miR-30b-5p and miR-320a shared the same target genes belonging to the RAS superfamily of small GTP-binding proteins (RAC1, RAP1A and RASA1), involved in neurotrophin-mediated cell survival. MiR-142, miR-135 and miR-320a in milk exosomes were the most responsive to group relocation of cows.

MiR-1246 is upregulated and regulates lung cell apoptosis during heat stress in feedlot cattle

Globally, heat stress seriously threatens productivity of cattle. The objective of this study was to identify novel miRNAs that regulated heat stress in feedlot cattle. Experiment was conducted under heat stress and normal conditions. With profiling miRNAs of each feedlot cattle, our results showed the level of miR-1246 was significantly increased in these heat-stressed cattle (P < 0.05). Furthermore, by using bioinformatics analysis and luciferase reporter assays combined with qPCR and western blot, we found miR-1246 negatively regulated poly (C) binding protein 2 (PCBP2) and cAMP response element binding protein-like 2 (CREBL2) mRNA and protein levels through binding to the 3'-UTR region (P < 0.05); further, it inhibited heat-induced apoptosis in lung cells. Finally, our results suggested that miR-1246 plays an important role in heat stress and it has the potential to be a novel modulation factor for heat stress in feedlot cattle.

In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle

The modern cattle was domesticated from aurochs, sharing its physiological traits into two subspecies Bos taurus and Bos indicus. MicroRNAs (miRNAs) are a class of non-coding short RNAs of ~22nt which have a key role in the regulation of many cellular and physiological processes in the animal. The current study was aimed to predict and annotate the potential mutations in indicine miRNAs throughout the genome using de novo and homology-based in silico approaches. Genome-wide mapping was performed in available indicine assembly by the homology-based approach and 768 miRNAs were recovered out of 808 reported taurine miRNAs belonging to 521 unique mature miRNA families. While 42 precursors were dropped due to lack of secondary miRNA structure, increasing stringency or decreasing similarity between the two genomes' miRNA. Increasing tendency of miRNAs incidence was observed on chr5, chr7, chr8, chr12 and chr21 with 19 polycistronic miRNA within 1-kilobase distance throughout the indicine genome. Notably, 12 miRNAs showed copy number variation. Eighteen miRNAs showed a mutation in their mature sequences in which eight were found in their seed region. Whilst in de novo based approach, 12 novel potential miRNAs on Y chromosome in indicine cattle along with a new miRNA (bind-miR-1264) on chrX were found. The final data set is annotated and explains the impending target genes that are responsible for enhanced immunity, heat tolerance and disease tolerance regulation in indicine. The study conforms to better understanding and perceptive approach towards indicine genome.

Identification of differentially expressed microRNAs in Sahiwal (Bos indicus) breed of cattle during thermal stress

microRNAs (miRNAs) are a class of small non-coding RNAs that play key roles in post transcriptional gene regulation that influence various fundamental cellular processes, including the cellular responses during environmental stresses. However, perusal of literatures revealed few reports on the differential expression of miRNA during thermal stress in Indian native (Bos indicus) cattle breeds. The present investigation aimed to identify differentially expressed miRNAs during thermal stress in Sahiwal (Bos indicus) dairy cattle breed of India, adapted with tropical climate over a long period of time. Stress responses of the animals were characterized by determining various physiological as well as biochemical parameters and differential expression profile of major heat shock protein genes. Ion Torrent deep sequencing and CLC-genomic analysis identified a set of differentially expressed miRNAs during summer and winter seasons. Most of the identified differentially expressed miRNAs were found to target heat shock responsive genes especially members of heat shock protein (HSP) family. Real-time quantification-based analysis of selected miRNAs revealed that bta-mir-1248, bta-mir-2332, bta-mir-2478, and bta-mir-1839 were significantly (p < 0.01) over expressed while bta-mir-16a, bta-let-7b, bta-mir-142, and bta-mir-425 were significantly (p < 0.01) under expressed during summer in comparison to winter. The present study enlists differentially expressed miRNAs at different environmental temperatures in Sahiwal (Bos indicus) that may be importance for further understanding the role of miRNAs on thermo-regulatory mechanisms.