Transcriptome analysis and identification of significantly differentially expressed genes in Holstein calves subjected to severe thermal stress

Differential gene expression analysis using RNA-seq in the blood of goats exposed to transportation stress

Transportation stress causes significant changes in physiological responses in goats; however, studies exploring the transcriptome of stress are very limited. The objective of this study was to determine the differential gene expressions and related pathways in the blood samples using RNA-seq procedure in Spanish goats subjected to different durations of transportation stress. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats/treatment): (1) transported for 180 min, (2) transported for 30 min, or (3) held in pens (control). Blood samples were collected before and after treatment for stress hormone, metabolite, and transcriptomic analysis. RNA-seq technology was used to obtain the transcriptome profiles of blood. Analysis of physiological data using SAS showed that plasma cortisol concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group. Enrichment analysis of DEGs related to transportation stress through Gene Ontology and KEGG databases revealed that the differentially expressed genes related to inflammatory pathways, caspases, and apoptosis such as IL1R2, CASP14, CD14, TLR4, and MAPK14 were highly enriched in the transported group of goats compared to non-transported goats. Stress in goats leads to a sequence of events at cellular and molecular levels that causes inflammation and apoptosis.

Identification of Novel mRNA Isoforms Associated with Acute Heat Stress Response Using RNA Sequencing Data in Sprague Dawley Rats

The molecular mechanisms underlying heat stress tolerance in animals to high temperatures remain unclear. This study identified the differentially expressed mRNA isoforms which narrowed down the most reliable DEG markers and molecular pathways that underlie the mechanisms of thermoregulation. This experiment was performed on Sprague Dawley rats housed at 22 °C (control group; CT), and three acute heat-stressed groups housed at 42 °C for 30 min (H30), 60 min (H60), and 120 min (H120). Earlier, we demonstrated that acute heat stress increased the rectal temperature of rats, caused abnormal changes in the blood biochemical parameters, as well as induced dramatic changes in the expression levels of genes through epigenetics and post-transcriptional regulation. Transcriptomic analysis using RNA-Sequencing (RNA-Seq) data obtained previously from blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120) was performed. The differentially expressed mRNA isoforms (DEIs) were identified and annotated by the CLC Genomics Workbench. Biological process and metabolic pathway analyses were performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 225, 5764, and 4988 DEIs in the blood, liver, and adrenal glands were observed. Furthermore, the number of novel differentially expressed transcript lengths with annotated genes and novel differentially expressed transcript with non-annotated genes were 136 and 8 in blood, 3549 and 120 in the liver, as well as 3078 and 220 in adrenal glands, respectively. About 35 genes were involved in the heat stress response, out of which, Dnaja1, LOC680121, Chordc1, AABR07011951.1, Hsp90aa1, Hspa1b, Cdkn1a, Hmox1, Bag3, and Dnaja4 were commonly identified in the liver and adrenal glands, suggesting that these genes may regulate heat stress response through interactions between the liver and adrenal glands. In conclusion, this study would enhance our understanding of the complex underlying mechanisms of acute heat stress, and the identified mRNA isoforms and genes can be used as potential candidates for thermotolerance selection in mammals.

Improving Genomic Selection for Heat Tolerance in Dairy Cattle: Current Opportunities and Future Directions

Heat tolerance is the ability of an animal to maintain production and reproduction levels under hot and humid conditions and is now a trait of economic relevance in dairy systems worldwide because of an escalating warming climate. The Australian dairy population is one of the excellent study models for enhancing our understanding of the biology of heat tolerance because they are predominantly kept outdoors on pastures where they experience direct effects of weather elements (e.g., solar radiation). In this article, we focus on evidence from recent studies in Australia that leveraged large a dataset [∼40,000 animals with phenotypes and 15 million whole-genome sequence variants] to elucidate the genetic basis of thermal stress as a critical part of the strategy to breed cattle adapted to warmer environments. Genotype-by-environment interaction (i.e., G × E) due to temperature and humidity variation is increasing, meaning animals are becoming less adapted (i.e., more sensitive) to changing environments. There are opportunities to reverse this trend and accelerate adaptation to warming climate by 1) selecting robust or heat-resilient animals and 2) including resilience indicators in breeding goals. Candidate causal variants related to the nervous system and metabolic functions are relevant for heat tolerance and, therefore, key for improving this trait. This could include adding these variants in the custom SNP panels used for routine genomic evaluations or as the basis to design specific agonist or antagonist compounds for lowering core body temperature under heat stress conditions. Indeed, it was encouraging to see that adding prioritized functionally relevant variants into the 50k SNP panel (i.e., the industry panel used for genomic evaluation in Australia) increased the prediction accuracy of heat tolerance by up to 10% units. This gain in accuracy is critical because genetic improvement has a linear relationship with prediction accuracy. Overall, while this article used data mainly from Australia, this could benefit other countries that aim to develop breeding values for heat tolerance, considering that the warming climate is becoming a topical issue worldwide.

Liver Transcriptome Response to Heat Stress in Beijing You Chickens and Guang Ming Broilers

Heat stress is one of the most prevalent issues in poultry production that reduces performance, robustness, and economic gains. Previous studies have demonstrated that native chickens are more tolerant of heat than commercial breeds. However, the underlying mechanisms of the heat tolerance observed in native chicken breeds remain unelucidated. Therefore, we performed a phenotypical, physiological, liver transcriptome comparative analysis and WGCNA in response to heat stress in one native (Beijing You, BY) and one commercial (Guang Ming, GM) chicken breed. The objective of this study was to evaluate the heat tolerance and identify the potential driver and hub genes related to heat stress in these two genetically distinct chicken breeds. In brief, 80 BY and 60 GM, 21 days old chickens were submitted to a heat stress experiment for 5 days (33 °C, 8 h/day). Each breed was divided into experimental groups of control (Ctl) and heat stress (HS). The results showed that BY chickens were less affected by heat stress and displayed reduced DEGs than GM chickens, 365 DEGs and 382 DEGs, respectively. The transcriptome analysis showed that BY chickens exhibited enriched pathways related to metabolism activity, meanwhile GM chickens’ pathways were related to inflammatory reactions. CPT1A and ANGPTL4 for BY chickens, and HSP90B1 and HSPA5 for GM chickens were identified as potential candidate genes associated with HS. The WGCNA revealed TLR7, AR, BAG3 genes as hub genes, which could play an important role in HS. The results generated in this study provide valuable resources for studying liver transcriptome in response to heat stress in native and commercial chicken lines.

Heat stress and immune response phenotype affect DNA methylation in blood mononuclear cells from Holstein dairy cows

Heat stress negatively affects health and production in cows. Examining the cellular response to heat stress could reveal underlying protective molecular mechanisms associated with superior resilience and ultimately enable selection for more resilient cattle. This type of investigation is increasingly important as future predictions for the patterns of heat waves point to increases in frequency, severity, and duration. Cows identified as high immune responders based on High Immune Response technology (HIR) have lower disease occurrence compared to their average and low immune responder herd-mates. In this study, our goal was to identify epigenetic differences between high and low immune responder cows in response to heat stress. We examined genome-wide DNA methylation of blood mononuclear cells (BMCs) isolated from high and low cows, before and after in vitro heat stress. We identified differential methylation of promoter regions associated with a variety of biological processes including immune function, stress response, apoptosis, and cell signalling. The specific differentially methylated promoter regions differed between samples from high and low cows, and results revealed pathways associated with cellular protection during heat stress.

Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

Background

Heat stress (HS) is a major stress event in the life of an animal, with detrimental upshots in production and health. Long-non-coding RNAs (lncRNAs) play an important role in many biological processes by transcriptional regulation. However, no research has been reported on the characterization and functionality of lncRNAs in heat-stressed rats.

Results

We studied expression levels of lncRNAs in rats during HS, using strand-specific RNA sequencing. Six rats, three in each of Control (22 ± 1 °C) and H120 (42 °C for 120 min) experimental groups, were used to screen for lncRNAs in their liver and adrenal glands. Totally, 4498 and 7627 putative lncRNAs were identified in liver and adrenal glands of the Control and H120 groups, respectively. The majority of lncRNAs were relatively shorter and contained fewer exons than protein-coding transcripts. In total, 482 (174 up-regulated and 308 down-regulated) and 271 (126 up-regulated and 145 down-regulated) differentially-expressed lncRNAs (DElncRNAs, P < 0.05) were identified in the liver and adrenal glands of the Control and H120 groups, respectively. Furthermore, 1274, 121, and 73 target differentially-expressed genes (DEGs) in the liver were predicted to interact with DElncRNAs based on trans−/cis- and sequence similarity regulatory modes. Functional annotation analyses indicated that these DEGs were mostly significantly enriched in insulin signalling, myeloid leukaemia, and glucagon signalling pathways. Similarly, 437, 73 and 41 target DEGs in the adrenal glands were mostly significantly enriched in the cell cycle (trans-prediction) and lysosome pathways (cis-prediction). The DElncRNAs interacting with DEGs that encode heat shock proteins (HSPs) may play an important role in HS response, which include Hsf4, Dnaja1, Dnajb4, Hsph1 and Hspb1 in the liver, and Dnajb13 and Hspb8 in the adrenal glands. The strand-specific RNA sequencing findings were also further verified through RT-qPCR.

Conclusions

This study is the first to provide a detailed characterization and functional analysis of expression levels of lncRNAs in liver and adrenal glands of heat-stressed rats, which provides basis for further studies on the biological functions of lncRNAs under heat stress in rats and other mammalian species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07421-8.

Genome-Wide Transcriptome and Metabolome Analyses Provide Novel Insights and Suggest a Sex-Specific Response to Heat Stress in Pigs

Heat stress (HS) negatively impacts pig production and swine health. Therefore, to understand the genetic and metabolic responses of pigs to HS, we used RNA-Seq and high resolution magic angle spinning (HR-MAS) NMR analyses to compare the transcriptomes and metabolomes of Duroc pigs (n = 6, 3 barrows and 3 gilts) exposed to heat stress (33 °C and 60% RH) with a control group (25 °C and 60% RH). HS resulted in the differential expression of 552 (236 up, 316 down) and 879 (540 up, 339 down) genes and significant enrichment of 30 and 31 plasma metabolites in female and male pigs, respectively. Apoptosis, response to heat, Toll-like receptor signaling and oxidative stress were enriched among the up-regulated genes, while negative regulation of the immune response, ATP synthesis and the ribosomal pathway were enriched among down-regulated genes. Twelve and ten metabolic pathways were found to be enriched (among them, four metabolic pathways, including arginine and proline metabolism, and three metabolic pathways, including pantothenate and CoA biosynthesis), overlapping between the transcriptome and metabolome analyses in the female and male group respectively. The limited overlap between pathways enriched with differentially expressed genes and enriched plasma metabolites between the sexes suggests a sex-specific response to HS in pigs.

Heat Stress Impairs the Physiological Responses and Regulates Genes Coding for Extracellular Exosomal Proteins in Rat

Heat stress (HS) is challenging in humans and animals as it is a complicated regulatory mechanism. This prompted us to characterize the physiological and molecular responses of a HS-animal model. In this study, a rat model system was developed by using three temperature treatments (40 ℃, 42 ℃, and 43 ℃) and sixteen biochemical indicators in blood at 42 ℃ for 30 min (H30), 60 min (H60), and 120 min (H120). In addition, transcriptomic profiling was carried out in H120-rats’ blood, liver, and adrenal gland samples for detection of the genes of interest. Our findings demonstrated that the adrenocorticotropic hormone, catalase, prolactin, growth hormone, and lactic acid have significant spatiotemporal variation in the H120-rats as compared with the control. Furthermore, through transcriptomic screening, we documented a high ratio of differentially expressed genes (DEGs) in adrenal glands, liver, and blood, respectively. Among them, Nup153, Plxnb2, Stx7, Hspa9, Chordc1, Pde4d, Gm2α, and Rnf125 were associated with the regulation of HS and immune response processes. Notably, 36 and 314 of DEGs in blood and adrenal glands were detected in the composition of the extracellular exosome, respectively. Furthermore, the correlation analysis between gene transcripts and biochemical indicator levels identified the Lgals3, S1006, Fn1,F2, and Kng1l1 as key candidate genes for HS encoding extracellular exosomal proteins. On the basis of our results, it was concluded that the current rat model provides a molecular basis for future research in HS resistance in humans and livestock.

Transcriptome Analysis Reveals Potential Regulatory Genes Related to Heat Tolerance in Holstein Dairy Cattle

Heat stress affects the physiology and production performance of Chinese Holstein dairy cows. As such, the selection of heat tolerance in cows and elucidating its underlying mechanisms are vital to the dairy industry. This study aimed to investigate the heat tolerance associated genes and molecular mechanisms in Chinese Holstein dairy cows using a high-throughput sequencing approach and bioinformatics analysis. Heat-induced physiological indicators and milk yield changes were assessed to determine heat tolerance levels in Chinese Holstein dairy cows by Principal Component Analysis method following Membership Function Value Analysis. Results indicated that rectal temperature (RT), respiratory rate (RR), and decline in milk production were significantly lower (p < 0.05) in heat tolerant (HT) cows while plasma levels of heat shock protein (HSP: HSP70, HSP90), and cortisol were significantly higher (p < 0.05) when compared to non-heat tolerant (NHT) Chinese Holstein dairy cows. By applying RNA-Seq analysis, we identified 200 (81 down-regulated and 119 up-regulated) significantly (|log2fold change| ≥ 1.4 and p ≤ 0.05) differentially expressed genes (DEGs) in HT versus NHT Chinese Holstein dairy cows. In addition, 14 of which were involved in protein–protein interaction (PPI) network. Importantly, several hub genes (OAS2, MX2, IFIT5 and TGFB2) were significantly enriched in immune effector process. These findings might be helpful to expedite the understanding for the mechanism of heat tolerance in Chinese Holstein dairy cows.

Cardiac and Skeletal Muscle Transcriptome Response to Heat Stress in Kenyan Chicken Ecotypes Adapted to Low and High Altitudes Reveal Differences in Thermal Tolerance and Stress Response

Heat stress (HS) negatively affects chicken performance. Agricultural expansion will happen in regions that experience high ambient temperatures, where fast-growing commercial chickens are vulnerable. Indigenous chickens of such regions, due to generations of exposure to environmental challenges, might have higher thermal tolerance. In this study, two indigenous chicken ecotypes, from the hot and humid Mombasa (lowland) and the colder Naivasha (highland) regions, were used to investigate the effects of acute (5 h, 35°C) and chronic (3 days of 35°C for 8 h/day) HS on the cardiac and skeletal muscle, through RNA sequencing. The rectal temperature gain and the number of differentially expressed genes (DEGs) [False Discovery Rate (FDR) < 0.05] were two times higher in the acute stage than in the chronic stage in both ecotypes, suggesting that cyclic exposure to HS can lead to adaptation. A tissue- and stage-specific difference in response to HS was observed, with peroxisome proliferator-activated-receptor (PPAR) signaling and mitogen-activate protein kinase (MAPK) signaling pathways, enriched in heart and skeletal muscle, respectively, and the p53 pathway enriched only in the acute stage in both tissues. The acute and chronic stage DEGs were integrated by a region-specific gene coexpression network (GCN), and genes with the highest number of connections (hub genes) were identified. The hub genes in the lowland network were CCNB2, Crb2, CHST9, SESN1, and NR4A3, while COMMD4, TTC32, H1F0, ACYP1, and RPS28 were the hub genes in the highland network. Pathway analysis of genes in the GCN showed that p53 and PPAR signaling pathways were enriched in both low and highland networks, while MAPK signaling and protein processing in endoplasmic reticulum were enriched only in the gene network of highland chickens. This shows that to dissipate the accumulated heat, to reduce heat induced apoptosis, and to promote DNA damage repair, the ecotypes activated or suppressed different genes, indicating the differences in thermal tolerance and HS response mechanisms between the ecotypes. This study provides information on the HS response of chickens, adapted to two different agro climatic environments, extending our understanding of the mechanisms of HS response and the effect of adaptation in counteracting HS.

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.

Heat Stress-Responsive Transcriptome Analysis in the Liver Tissue of Hu Sheep

Heat stress has a severe effect on animal health and can reduce the productivity and reproductive efficiency; it is therefore necessary to explore the molecular mechanism involved in heat stress response, which is helpful for the cultivation of an animal breed with resistance to heat stress. However, little research about heat stress-responsive molecular analysis has been reported in sheep. Therefore, in this study, RNA sequencing (RNA-Seq) was used to investigate the transcriptome profiling in the liver of Hu sheep with and without heat stress. In total, we detected 520 and 22 differentially expressed mRNAs and lncRNAs, respectively. The differentially expressed mRNAs were mainly associated with metabolic processes, the regulation of biosynthetic processes, and the regulation of glucocorticoid; additionally, they were significantly enriched in the heat stress related pathways, including the carbon metabolism, the PPAR signaling pathway, and vitamin digestion and absorption. The co-located differentially expressed lncRNA Lnc_001782 might positively influence the expression of the corresponding genes APOA4 and APOA5, exerting co-regulative effects on the liver function. Thus, we made the hypothesis that Lnc_001782, APOA4 and APOA5 might function synergistically to regulate the anti-heat stress ability in Hu sheep. This study provides a catalog of Hu sheep liver mRNAs and lncRNAs, and will contribute to a better understanding of the molecular mechanism underlying heat stress responses.

Tracking transcriptomic responses to endogenous and exogenous variation in cetaceans in the Southern California Bight

Marine wildlife populations are adapted to survive in highly dynamic environments. However, identifying the effects of endogenous versus exogenous variables on marine mammal physiology remains a substantial challenge in part because of the logistical constraints that limit the collection of physiological data in free-ranging animals. Measuring genome-wide gene expression is one minimally invasive method that can be used to elucidate how free-ranging cetaceans' physiological responses shift with changing environmental conditions or demographic states, i.e. reproductive status and maturity. We identified transcriptomic differences among bottlenose dolphins (Tursiops truncatus) from the Southern California Bight using RNAseq data from the skin of 75 individuals to examine gene expression associated with sex, pregnancy status, sea surface temperature, geographic location and ecotype. We identified transcriptomic variation between two genetically distinct ecotypes as well as variation related to environmental conditions among groups that exhibit little evidence of genetic divergence. Specifically, we found differential expression of genes associated with structural development, cellular starvation and immune response. Sex and pregnancy status explained a small proportion of the observed variation, in contrast to sea surface temperature, which explained a substantial amount of transcriptomic variation. However, these measured variables did not account for all of the differential expression observed between ecotypes and among geographically distinct groups. Additional research is needed to identify other endogenous or exogenous factors that may be contributing to observed transcriptomic differences among ecotypes.

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.

Transcriptomic Analysis Reveals Insights on Male Infertility in Octopus maya Under Chronic Thermal Stress

Octopus maya endemic to the Yucatan Peninsula, Mexico, is an ectotherm organism particularly temperature-sensitive. Studies in O. maya females show that temperatures above 27°C reduce the number of eggs per spawn, fertilization rate and the viability of embryos. High temperatures also reduce the male reproductive performance and success. However, the molecular mechanisms are still unknown. The transcriptomic profiles of testes from thermally stressed (30°C) and not stressed (24°C) adult male octopuses were compared, before and after mating to understand the molecular bases involved in the low reproductive performance at high temperature. The testis paired-end cDNA libraries were sequenced using the Illumina MiSeq platform. Then, the transcriptome was assembled de novo using Trinity software. A total of 53,214,611 high-quality paired reads were used to reconstruct 85,249 transcripts and 77,661 unigenes with an N50 of 889 bp length. Later, 13,154 transcripts were annotated implementing Blastx searches in the UniProt database. Differential expression analysis revealed 1,881 transcripts with significant difference among treatments. Functional annotation and pathway mapping of differential expressed transcripts revealed significant enrichment for biological processes involved in spermatogenesis, gamete generation, germ cell development, spermatid development and differentiation, response to stress, inflammatory response and apoptosis. Remarkably, the transcripts encoding genes such as ZMYND15, KLHL10, TDRD1, TSSK2 and DNAJB13, which are linked to male infertility in other species, were differentially expressed among the treatments. The expression levels of these key genes, involved in sperm motility and spermatogenesis were validated by quantitative real-time PCR. The results suggest that the reduction in male fertility at high temperature can be related to alterations in spermatozoa development and motility.