Novel SNPs in HSP70A1A gene and the association of polymorphisms with thermo tolerance traits and tissue specific expression in Chinese Holstein cattle

Association analysis of HSP90AA1 polymorphism with thermotolerance in tropically adapted Indian crossbred cattle

Raising cattle is a lucrative business that operates globally but is confronted by many obstacles, such as thermal stress, which results in substantial monetary losses. A vital role of heat shock proteins (HSPs) is to protect cells from cellular damage. HSP90 is a highly prevalent, extremely adaptable gene linked to physiological resilience in thermal stress. This study aimed to find genetic polymorphisms of the HSP90AA1 gene in Karan Fries cattle and explore their relationship to thermal tolerance and production traits. One SNP (g.3292 A > C) was found in the Intron 8 and three SNPs loci (g.4776 A > G, g.5218T > C and g.5224 A > C) were found in the exon 11 of 100 multiparous Karan Fries cattle. The association study demonstrated that the SNP1-g.3292 A > C was significantly (P < 0.01) linked to the variables respiratory rate (RR), heat tolerance coefficient (HTC) and total milk yield (TMY (kg)) attributes. There was no significant correlation identified between any of the other SNP sites (SNP2-g.4776 A > G; SNP3-g.5218T > C; SNP4-g.5224 A > C) with the heat tolerance and production attributes in Karan Fries cattle. Haploview 4.2 and SHEsis software programs were used to analyse pair linkage disequilibrium and construct haplotypes for HSP90AA1. Association studies indicated that the Hap3 (CATA) was beneficial for heat tolerance breeding in Karan Fries cattle. In conclusion, genetic polymorphisms and haplotypes in the HSP90AA1 were associated with thermal endurance attributes. This relationship can be utilized as a beneficial SNP or Hap marker for genetic heat resistance selection in cow breeding platforms.

Intensity of estrus expression - valuable obvious determinant of fertility in Bos indicus cows

This study aimed to characterize estrus response and to establish relationships between intensity of estrus, preovulatory follicle (POF) size and estradiol (E2) concentrations on day of AI, luteal profiles and pregnancy outcome in lactating Hariana breed of cows. 200 cyclic cows were subjected to Ovsynch (n = 54) and Pre-OV treatment (n = 146). Ovsynch: Buserelin acetate (BA; 10 µg), Cloprostenol (500 µg) and BA (10 µg) were injected i.m. on day 0, 7 and 9, respectively, irrespective of treatment. Pre-OV: BA (10 µg) and Cloprostenol (500 µg) was also injected i.m. simultaneously 7 days prior to initiate Ovsynch. On the basis of estrus behavior, the cows were classified into three groups: weak, moderate and intense. Artificial insemination performed at 18-24 hours after 2nd BA of Ovsynch in both treatments. The average duration of estrus did not differ (p > 0.05) between Ovsynch and Pre-OV treatment. A positive correlation was observed between estrus response and POF size, concentration of E2 on day of AI and luteal profiles on day 12 post-AI. First service conception rate was higher in cows exhibited intense (45.46%) and moderate (42.56%) estrus response than weak (28.57%) estrus response. In conclusion, intensity of estrus expression could be considered as important determinant for deciding pregnancy outcomes in Bos indicus cows.

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.

A novel SNP of TECPR2 gene associated with heat tolerance in Chinese cattle

Heat stress affects the animal production and causes serious economic losses to the husbandry. Tectonin beta-propeller repeat containing 2 (TECPR2) gene plays an important role in autophagy which may affect the temperature sensation in animals. A missense mutation (XM_024981840.1:c.3989 G > A p.Arg1330His) of the transcripts X4 in the bovine TECPR2 gene was identified. In this study, the c.3989 G > A variant in TECPR2 gene was genotyped in a total of 25 cattle breeds (520 individuals). Our results indicated that the frequency of A allele showed a decreasing pattern from southern cattle to northern cattle, while the frequency of G allele showed the opposite pattern, which was consistent with the climate distribution of China. Compared with the GG genotype, southern cattle carried more the AA and AG genotypes. Furthermore, the association results carried out that the frequencies of genotypes (GG, AG, AA) and the value of climate parameters (mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) were significantly correlated (p < 0.01). Hence, we speculated that the c.3989 G > A variant of TECPR2 gene was associated with the heat tolerance trait in Chinese cattle and the locus may be considered as a molecular marker for Chinese cattle breeding.

Heat Stress: A Serious Disruptor of the Reproductive Physiology of Dairy Cows

Global warming is a significant threat to the sustainability and profitability of the dairy sector, not only in tropical or subtropical regions but also in temperate zones where extreme summer temperatures have become a new and challenging reality. Prolonged exposure of dairy cows to high temperatures compromises animal welfare, increases morbidity, and suppresses fertility, resulting in devastating economic losses for farmers. To counteract the deleterious effects of heat stress, cattl e employ various adaptive thermoregulatory mechanisms including molecular, endocrine, physiological, and behavioral responses. These adaptations involve the immediate secretion of heat shock proteins and cortisol, followed by a complex network of disrupted secretion of metabolic and reproductive hormones such as prolactin, ghrelin, ovarian steroid, and pituitary gonadotrophins. While the strategic heat stress mitigation measures can restore milk production through modifications of the microclimate and nutritional interventions, the summer fertility records remain at low levels compared to those of the thermoneutral periods of the year. This is because sustainment of high fertility is a multifaceted process that requires appropriate energy balance, undisrupted mode of various hormones secretion to sustain the maturation and fertilizing competence of the oocyte, the normal development of the early embryo and unhampered maternal-embryo crosstalk. In this review, we summarize the major molecular and endocrine responses to elevated temperatures in dairy cows, as well as the impacts on maturing oocytes and early embryos, and discuss the consequences that heat stress brings about in dairy cattle fertility.

Genetic studies of heat stress regulation in goat during hot climatic condition

Various direct and indirect environmental constraints have an impact on livestock performance. The physiological parameters, such as rectal temperature, heart rate, and respiratory rate, are the primary indicators of thermal stress. Under a stressed environment temperature humidity index (THI) had established as a vital measurement to identify the thermal stress in livestock. THI in association with climatic variations can define the environmental effect as stressful or comfortable for livestock. Goats are small ruminants that adapt to a wide range of ecological variations due to their anatomical and physiological characteristics. However, the productivity of animals declines at the individual level during thermal stress. Stress tolerance can be determined through genetic studies associated with at the cellular level using physiological as well as molecular approaches. Information on genetic association with thermal stress in goats is scanty, this severely affects their survival and hence productivity of livestock. The ever-increasing demand for food across the globe needs deciphering novel molecular markers as well as stress indicators that play a vital role in livestock improvement. This review represents an analysis of current knowledge of phenotypic differences during thermal stress and signifies the importance of physiological responses and their association at the cellular level in goats. The regulation of vital genes associated with thermal stress such as Aquaporins (AQP 0, 1, 2, 4, 5, 6, 8), aquaglyceroporins (AQP3, 7, 9, and 10) and super-aquaporins (AQP 11, 12); BAX inhibitors such as PERK (PKR like ER kinase), IRE 1(inositol-requiring-1); Redox regulating genes such as NOX; Transport of Na+ and K+ such as ATPase (ATP1A1) and several heat shock proteins have been implicated in heat-stress related adaptations have been elucidated. As these changes have a significant impact on production performance as well as on livestock productivity. Such efforts may help in the development of molecular markers and will assist the breeders to develop heat-tolerant goats with improved productivity.

The profile of HSPA1A gene expression and its association with heat tolerance in crossbred cattle and the tropically adapted dwarf Vechur and Kasaragod

Certain livestock breeds are adapted to hot and humid environments, and these breeds have genetics that could be useful in a changing climate. The expression of several genes has been identified as a useful biomarker for heat stress. In this study, the responses to heat exposure of heat-tolerant Vechur and Kasaragod cattle found in Kerala state in India (also known as dwarf Bos taurus indicus) were compared to crossbred cattle (crosses of Bos t. taurus with Bos t. indicus). At various time points during heat exposure, rectal temperature and the expression of HSPA1A were determined, and the relationship between them was characterized. We characterized HSPA1A mRNA in Vechur cattle and performed molecular clock analysis. The expression of HSPA1A between the lineages and at different temperature humidity index (THI) was significant. There were significant differences between the expression profiles of HSPA1A in Kasaragod and crossbred (p < 0.01) and Vechur and crossbred (p < 0.01) cattle, but no significant difference in expression was observed between Vechur and Kasaragod cattle. The genetic distance between Vechur, B. grunniens, B. t. taurus, and B. t. indicus was 0.0233, 0.0059, and 0.007, respectively. The genetic distance between Vechur and the Indian dwarf breed Malnad Gidda was 0.0081. A molecular clock analysis revealed divergent adaptive evolution of Vechur cattle to B. t. taurus, with adaptations to the high temperatures and humidity that are prevalent in their breeding tract in Kerala, India. These results could also prove useful in selecting heat-tolerant animals using HSPA1A as a marker.

Presynchronization with simultaneous administration of GnRH and prostaglandin F2α (PGF2α) 7 days prior to Ovsynch improves reproductive profile in Hariana zebu cow

This study is aimed at assessing the impact of simultaneous administration of GnRH and prostaglandin F_2α (PGF_2α) 7 days prior to Ovsynch in Hariana cow. Two hundred cyclic cows (> 4 months postpartum) were assigned to control (n = 54) and pre-OV (n = 146). As per Ovsynch protocol, buserelin acetate (10 μg), cloprostenol (500 μg), and buserelin acetate (10 μg) were injected i.m. on days 0, 7, and 9, respectively, in cows irrespective of treatment. But in pre-OV cows, buserelin acetate (10 μg) and cloprostenol (500 μg) were also injected i.m. simultaneously 7 days prior to initiate the Ovsynch protocol. Artificial insemination was performed between 18 and 24 h after the 2nd GnRH of Ovsynch in both treatments. Ultrasonography and blood sampling for hormonal analysis were done on each day of treatment, on day of AI, and 12 days post-AI. Pre-OV treatment resulted to increased (45.20% vs 29.62%; P < 0.05) pregnancy outcomes and higher (P < 0.01) ovulation rate to first GnRH of Ovsynch than control. Cows showing complete luteolysis in response to PGF_2α of Ovsynch were also higher (P < 0.05) in pre-OV than control. Greater (P < 0.05) synchronization rate was recorded in pre-OV than control (86.76% and 68.75%). The circulating concentrations of estradiol on day of AI and progesterone on day 12 post-AI were higher (P < 0.01) in cows diagnosed pregnant than non-pregnant in both control and pre-OV treatment. In conclusion, simultaneous administration of GnRH and PGF_2α 7 days before Ovsynch improved the synchronization rate and luteal profile in terms of CL area and hence resulted in higher conception rate in Hariana zebu cow.

Whole-Genome comparative analysis reveals genetic mechanisms of disease resistance and heat tolerance of tropical Bos indicus cattle breeds

The Bos indicus cattle breeds have been naturally selected over thousands of years for disease resistance and thermo-tolerance. However, a genetic mechanism of these specific inherited characteristics needs to be discovered. Hence, in this study, the whole-genome comparative analysis of Bos indicus cattle breeds of Kangayam, Tharparkar, Sahiwal, Red Sindhi, and Hariana of the Indian subcontinent was conducted. The genetic variants identification analysis revealed a total of 15,58,51,012 SNPs and 1,00,62,805 InDels in the mapped reads across all Bos indicus cattle breeds. The functional annotation of 17,252 genes that comprised both, SNPs and InDels, of high functional impact on proteins, has been carried out. The functional annotation results revealed the pathways that were involved in the innate immune response including toll-like receptors, a retinoic acid-inducible gene I like receptors, NOD-like receptors, Jak-STAT signaling pathways, and the non-synonymous variants in the candidate immune genes. Further, we also identified several pathways involved in heat shock response, hair and skin properties, oxidative stress response, osmotic stress response, thermal sweating, feed intake, metabolism, and the non-synonymous variants in the candidate thermo-tolerant genes. These pathways and genes were directly or indirectly contributing to the disease resistance and thermo-tolerance adaptations of Bos indicus cattle breeds.

Heterozygous Single-Nucleotide Polymorphism Genotypes at Heat Shock Protein 70 Gene Potentially Influence Thermo-Tolerance Among Four Zebu Breeds of Nigeria

Genetic variants at heat shock protein 70 gene and their influence on heat stress (HS) tolerance were studied among selected Nigeria zebu, namely, 25 White Fulani (WF), 21 Sokoto Gudali (SG), 21 Red Bororo (RB), and 23 Ambala (AM). Detection of single nucleotide polymorphism (SNP) followed by determination of genotype and genotypic frequency was made among the selected breeds. The heat tolerance coefficient (HTC) was determined from thermo-related parameters including body temperature, rectal temperature, and respiratory rate. Thermo-Tolerance was evaluated through the SNP-thermo-parameter relationship. Statistical analyses were done using the GLM procedure in SAS. A quantitative real-time/high-resolution melting-based assay detected twelve genetic variants. Five of these were common and shared across all breeds of cattle. Of the remaining seven variants, three were specifically identified in AM, two in SG, and two in RB. Also, SNPs were evaluated and four unique SNPs (C151T, C146T, G90A, and C219A) were identified. Heterozygous animals had lower HTC suggesting their potential to withstand HS than homozygous counterparts. The WF and RB animals had significantly lower values for all parameters (BT, RT, RR, and HTC) compared to AM and SG breeds. Thermo-related parameters were significantly different (P < 0.001), and it is recommended that screening of SNPs in zebu is needed to enable selection for improved thermo-tolerance.

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.

Genomic regions and pathways associated with thermotolerance in layer-type strain Taiwan indigenous chickens

This study aimed to investigate genetic markers and candidate genes associated with thermotolerance in a layer-type strain Taiwan indigenous chickens exposed to acute heat stress. One hundred and ninety-two 30-week-old roosters were subjected to acute heat stress. Changes in body temperature (BT, ΔT) were calculated by measuring the difference between the initial BT and the highest BT during heat stress and the results were categorized into dead, susceptible, tolerant, and intermediate groups depending on their survival and ΔT values at the end of the experiment. A genome-wide association study on survival and ΔT values was conducted using the Cochran-Armitage trend test and Fisher's exact test. Association analyses identified 80 significant SNPs being annotated to 23 candidate genes, 440 SNPs to 71 candidate genes, 64 SNPs to 25 candidate genes, and 378 SNPs to 78 candidate genes in the dead versus survivor, tolerant versus susceptible, intermediate versus tolerant, and intermediate versus susceptible groups, respectively. The annotated genes were associated with apoptosis, cellular stress responses, DNA repair, and metabolic oxidative stress. In conclusion, the identified SNPs of candidate genes provide insights into the potential mechanisms underlying physiological responses to acute heat stress in chickens.

Genetic profiling of Hsp70 gene in Murrah buffalo (Bubalus bubalis) under sub-tropical climate of India

This study was aimed to genetic profiling of heat shock protein 70 (Hsp70) gene in Murrah buffalo investigating 50 unrelated adult animals at ICAR-Research Complex for Eastern Region, Patna (India) in winter, spring, and summer. PCR ready genomic DNA samples and season-wise total RNA samples were prepared. The PCR products of Hsp70 eluted from agarose gel were sequenced and analyzed. The first-strand cDNA was synthesized and concentration was equalized to 25 ng/μl. Expression kinetics of mRNA transcripts in different seasons was studied using Brilliant SYBR Green QPCR technique and the data retrieved was analyzed by least-squares ANOVA. DNA sequencing by primer walking revealed four allelic variants of Hsp70 gene. Alignment study revealed one substitution in 5'UTR, six substitutions in coding region, and one addition in 3'UTR. The highest percent identity and negligible phylogenetic distance were found among the alleles and reference bovine sequences. The relative mRNA expression was significantly higher in summer when THI ≥ 84 than the spring and winter; fold change increased by 4.5 times in summer than the spring whereas found nearly half in winter. These findings can be useful for heat stress management in buffaloes and help in understanding the mechanism of thermo-regulation well.

Characterizing binding sites of heat responsive microRNAs and their expression pattern in heat stressed PBMCs of native cattle, exotic cattle and riverine buffaloes

It is generally believed that due to evolutionary differences and adaptation to tropical conditions, Indian native cattle has superior heat tolerant ability than Bos taurus cattle. In the present study, 3'-UTR of two most important heat responsive genes i.e., heat shock protein 70.1 (HSP70.1) and heat shock factor- 1 (HSF-1) were sequence characterized in different breeds of Indian native cattle to identify the variations and miRNA binding sites. In addition, the impact of heat stress was assessed in a total of 57 PBMCs samples of native Sahiwal cows (Bos indicus), exotic Holstein cows (Bos taurus) and Murrah buffaloes (Bubalus bubalis) using various cellular parameters like cell viability, cytotoxicity and apoptosis. Further, expression profile of 12 heat responsive miRNAs were also evaluated in unstressed and stressed PBMCs to understand post transcriptional changes in native cows, exotic cows and Murrah buffaloes. The sequence data showed 3'-UTR of HSP70.1 gene of Indian cattle to be exactly similar to Bos taurus with no miRNA binding site. Whereas, sequencing of 3'-UTR of HSF-1 gene revealed 3 SNPs at positions G1762T; C1811T and C1983T with 7 well conserved miRNA binding sites. The impact of heat stress on various cellular parameters in terms of cell viability, cytotoxicity and apoptosis was highest in PBMCs of Holstein cows followed by Murrah buffaloes and Sahiwal cows. Further, in contrast to Holstein Frisian cows and Murrah buffaloes, the expression pattern of 12 heat responsive miRNAs, in heat stressed PBMCs of Sahiwal cows were quite distinct. There was a significant (p < 0.05) induction in expression of most of the miRNAs after heat stress in PBMCs of Sahiwal cows followed by a rapid decline. The distinct cellular response and pattern of miRNA expression across cattle types and buffaloes might be influencing their PBMCs tolerance level to heat stress.

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.

A Missense Mutation of the HSPB7 Gene Associated with Heat Tolerance in Chinese Indicine Cattle

Simple Summary

A missense mutation (NC_037329.1: g.136054902 C > G: p. Ala69Gly) was identified in the heat shock protein family B (small) member 7 (HSPB7) gene in indicine cattle, which might be a candidate mutation associated with the heat tolerance. Here, Polymerase Chain Reaction and DNA sequencing methods were used to detect this mutation in 774 individuals belonging to 32 Chinese indigenous cattle breeds. The distribution of alleles of NC_037329.1: g.136054902 C > G displays significant geographical difference across native Chinese cattle breeds and cattle carrying allele G distributed in regions with higher mean annual temperature, relative humidity, and temperature humidity index. Our results demonstrate that the mutation of the HSPB7 gene in Chinese indicine cattle might be a candidate gene associated with the heat tolerance.

Abstract

The small heat shock proteins (HSPB) are expressed in response to heat stress, and the heat shock protein family B (small) member 7 (HSPB7) gene has been reported to play an important role in heat tolerance pathways. Only a missense mutation (NC_037329.1: g.136054902 C > G: p.Ala69Gly) was identified in the HSPB7 gene in indicine cattle, which might be a candidate mutation associated with the heat tolerance. Here, we explore the allele frequency of this mutation in 774 individuals belonging to 32 Chinese indigenous cattle breeds using polymerase chain reaction (PCR) and DNA sequencing methods. The distribution of alleles of NC_037329.1: g.136054902 C > G displays significant geographical difference across native Chinese cattle breeds that the allele C was dominant in northern cattle groups, while allele G was dominant in southern indicine cattle groups. Additionally, the association analysis indicated that the G allele was significantly associated with mean annual temperature (T), relative humidity (RH), and temperature humidity index (THI) (p < 0.01), suggesting that cattle carrying allele G were distributed in regions with higher T, RH, and THI. Our results demonstrate that the mutation of the HSPB7 gene in Chinese indicine cattle might be a candidate gene associated with the heat tolerance.

Detection of functional polymorphisms in the hsp70 gene and association with cold stress response in Inner-Mongolia Sanhe cattle

The genetic mechanisms underlying the cattle resilience to severe cold temperatures are still unknown. In this study, we observed that four blood biochemical parameters were significantly altered, i.e., blood adrenocorticotropic hormone (ACTH), triiodothyronine (T3), thyroxine (T4), and potassium (K+) after expose to - 32 °C for 3 h. This was observed using 105 healthy Sanhe heifers with similar weight (398.17 ± 34.06 kg) and age (19.30 ± 4.91 months). A total of 20 single nucleotide polymorphisms (SNPs) were identified in 5'-flanking region of the hsp70 gene in Sanhe cattle, while only 10 SNPs were segregating when comparing genetic variations between Sanhe cattle and 285 Chinese Holstein samples. Statistically significant associations between the genomic markers SNP-42-, SNP-105+, SNP-181+, and SNP-205+ with blood T3 and between SNP-105+ and blood T4 were observed by applying the general linear model procedure and Bonferroni t test. Furthermore, we demonstrated that the T alleles of SNP-42- and SNP-205+ in the GC box and Kozak sequence of the hsp70 gene, respectively, significantly decreased the green fluorescent proteins activity in vitro GFP reporter assays. These findings suggest that these two SNPs are causative polymorphisms involved in the regulation of hsp70 promoter activity and might contribute to the observed association between the hsp70 gene and T3 and T4 levels in Sanhe cattle. Thus, hsp70 gene is a promising candidate gene to be validated in independent cattle populations and functional studies related to cold stress resilience in cattle.

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.

Identification and analysis of differentially expressed long non-coding RNAs of Chinese Holstein cattle responses to heat stress

The mechanisms that dairy cattle respond to environmental stresses are very complicated. Previous research into the molecular mechanisms of mammalian heat stress has largely focused on the role of protein-coding genes and small non-coding RNAs. Recently, it has become apparent that large numbers of long non-coding RNAs transcribed from mammalian genomes play extensive roles in transcriptional regulation. However, the expression of lncRNAs and their biological functions in heat stress in dairy cattle remain unknown. In this study, we employed a deep RNA sequencing to examine lncRNA expression profiles of heat stressed and non-heat stressed Chinese Holstein cattle. We found that 24,795 novel and 3763 known lncRNAs were expressed in the bovine mammary gland, of which 174 were differentially expressed in heat stress condition, among them, 156 lncRNAs were up-regulated and 18 were down-regulated. Through Cis role analysis, 16,474 lncRNAs were transcribed close to protein-coding neighbors. In addition, 11 and 2024 lncRNAs harbored precursors of known and predicted microRNAs, respectively, were annotated in the precursor analysis of miRNAs. Taken together, our findings represent the first systematic investigation of lncRNA expression in heat stressed Chinese Holstein and provide a resource for further research into the molecular mechanisms of lncRNAs function in dairy cattle.

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

RNA-Seq analysis was used to characterize transcriptome response of Holstein calves to thermal stress. A total of eight animals aged between 2 and 3 months were randomly selected and subjected to thermal stress corresponding to a temperature humidity index of 95 in an environmentally controlled house for 12 h consecutively for 3 days. A set of 15,787 unigenes were found to be expressed and after a threshold of threefold change, and a Q value <0.05; 502, 394, and 376 genes were found to be differentially expressed on days 1, 2, and 3 out of which 343, 261 and 256 genes were upregulated and 159, 133, and 120 genes were downregulated. Only 356 genes out of these were expressed on all 3 days, and only they were considered as significantly differentially expressed. KEGG pathway analysis revealed that ten pathways were significantly enriched; the top two among them were protein processing in endoplasmic reticulum and MAPK signaling pathways. These results suggest that thermal stress triggered a complex response in Holstein calves and the animals adjusted their physiological and metabolic processes to survive. Many of the genes identified in this study have not been previously reported to be involved in thermal stress response. The results of this study extend our understanding of the animal's response to thermal stress and some of the identified genes may prove useful in the efforts to breed Holstein cattle with superior thermotolerance, which might help in minimizing production loss due to thermal stress.

Characterization of genes and pathways that respond to heat stress in Holstein calves through transcriptome analysis

This study aimed to investigate the genes and pathways that respond to heat stress in Holstein bull calves exposed to severe ranges of temperature and humidity. A total of ten animals from 4 to 6 months of age were subjected to heat stress at 37 °C and 90 % humidity for 12 h. Skin and rectal temperatures were measured before and after heat stress; while no correlation was found between them before heat stress, a moderate correlation was detected after heat stress, confirming rectal temperature to be a better barometer for monitoring heat stress. RNAseq analysis identified 8567 genes to be differentially regulated, out of which 465 genes were significantly upregulated (≥2-fold, P < 0.05) and 49 genes were significantly downregulated (≤2-fold, P < 0.05) in response to heat stress. Significant terms and pathways enriched in response to heat stress included chaperones, cochaperones, cellular response to heat stress, phosphorylation, kinase activation, immune response, apoptosis, Toll-like receptor signaling pathway, Pi3K/AKT activation, protein processing in endoplasmic reticulum, interferon signaling, pathways in cancer, estrogen signaling pathway, and MAPK signaling pathway. The differentially expressed genes were validated by quantitative real-time PCR analysis, which confirmed the tendency of the expression. The genes and pathways identified in this analysis extend our understanding of transcriptional response to heat stress and their likely functioning in adapting the animal to hyperthermic stress. The identified genes could be used as candidate genes for association studies to select and breed animals with improved heat tolerance.

Impact of heat stress on health and performance of dairy animals: A review

Sustainability in livestock production system is largely affected by climate change. An imbalance between metabolic heat production inside the animal body and its dissipation to the surroundings results to heat stress (HS) under high air temperature and humid climates. The foremost reaction of animals under thermal weather is increases in respiration rate, rectal temperature and heart rate. It directly affect feed intake thereby, reduces growth rate, milk yield, reproductive performance, and even death in extreme cases. Dairy breeds are typically more sensitive to HS than meat breeds, and higher producing animals are, furthermore, susceptible since they generates more metabolic heat. HS suppresses the immune and endocrine system thereby enhances susceptibility of an animal to various diseases. Hence, sustainable dairy farming remains a vast challenge in these changing climatic conditions globally.

Novel SNP identification in exon 3 of HSP90AA1 gene and their association with heat tolerance traits in Karan Fries (Bos taurus × Bos indicus) cows under tropical climatic condition

Heat shock proteins (HSPs) act as molecular chaperones those are preferentially transcribed in respose to heat stress and the polymorphism in HSP genes associated with heat tolerance traits in cows. HSP90AA1 gene has been mapped on Bos taurus autosome 21 (BTA-21) and spans nearly 5368 bp comprising of 11 exons out of which the first exon does not translate. The present study was done on Karan Fries (5/8 HF × 3/8 Tharparkar) cows reared in tropical climate with the objectives of identifying single-nucleotide polymorphisms (SNPs) in targeted regions (exon 3) of HSP90AA1 gene and analyzing their association with heat tolerance traits in Karan Fries cows. Respiration rate (RR) and rectal temperature (RT) were recorded once daily for four consecutive days during probable extreme hours in different seasons or temperature humidity index (THI), viz., winter, spring, and summer. For detecting single-nucleotide polymorphisms, sequence data were analyzed using BioEdit software (version 7.2). Comparative sequence analysis of HSP90AA1 gene showed point mutation, viz., g.1209A>G (exon 3) as compared to Bos taurus (NCBI Ref Seq: AC_000178.1). Association analysis indicated that THI was influenced (P < 0.01) by RR, RT, and HTC. Similarly, SNPs at locus g.1209A>G were categorized into three genotypes, i.e., AA, AG, and GG, and the least squares means (LSMEANS) of RR, RT, and HTC for GG (homozygous) genotype were significantly lower (P < 0.01) than AA (homozygous) and AG (heterozygous) genotypes. These findings may partly suggest that cows with GG genotypes were favored for heat tolerance trait, which can be used as an aid to selection for thermo-tolerance Karan Fries cows for better adaptation in subtropical and tropical hot climate.

Effect of heat shock protein 70 polymorphism on thermotolerance in Tharparkar cattle

AIM

Out of various members of heat shock protein (HSP) superfamily which act a molecular chaperon by binding to the denaturing protein thus stabilizing them and preserving their activity, HSP70 are of major importance in thermotolerance development. Thus, present investigation aimed at a screening of HSP70 gene for polymorphisms and possible differences in thermotolerance in Tharparkar breed of cattle.

MATERIALS AND METHODS

A 295 bp fragment of HSP70 gene was subjected to polymerase chain reaction-single-strand conformation polymorphism (SSCP) followed by sequencing of different SSCP patterns in 64 Tharparkar cattle. A comparative thermotolerance of identified genotypes was analyzed using heat tolerance coefficients (HTCs) of animals for different seasons.

RESULTS

Three SSCP patterns and consequently two alleles namely A and B were documented in one fragment of HSP70 gene. On sequencing, one single-nucleotide polymorphism with G > T substitution was found at a position that led to a change of amino acid aspartate to tyrosine in allele A. It was found that in maintaining near normal average rectal temperature, genotype AA was superior (p≤0.01). Genotype AA, thus, was found to be most thermotolerant genotype with the highest HTC (p≤0.01).

CONCLUSION

The polymorphism at HSP70 is expected to be a potent determinant for heat tolerance in cattle, which may aid in selection for thermotolerance in cattle.

Seasonal changes in gene expression and polymorphism of hsp70 in cultivated oysters (Crassostrea gigas) at extreme temperatures

The HSP70 proteins are an important element of the response against thermal stress and infectious diseases, and they are highly conserved and ubiquitous. In some species, variations on the hsp70 encoding sequence resulted in intraspecific differential expression, which leads to variations on thermo-tolerance among individuals. This phenomenon has not been described in the Pacific oyster Crassostrea gigas, which is cultivated in Mexico under temperature conditions highly above the optimal for this species. The present study was aimed to identify associations between hsp70 genotypes and their expression levels in C. gigas. By analyzing a 603 bp fragment from the 3' end of the hsp70 gene, 21 different genotypes with 60 nucleotide polymorphic sites were detected, of which 34 sites were found in heterozygous condition. Although no correlation was found between genotype-expression-season, a minimum expression threshold that should be taken into account as an important feature for a future breeding program is proposed.

Association of ATP1A1 gene polymorphism with thermotolerance in Tharparkar and Vrindavani cattle

Aim:

One of the major biochemical aspects of thermoregulation is equilibrium of ion gradient across biological membranes. Na⁺/K⁺-ATPase, a member of P type-ATPase family, is a major contributor to the mechanism that actively controls cross-membrane ion gradient. Thus, we examined ATP1A1 gene that encodes alpha-1 chain of Na⁺/K⁺-ATPase, for genetic polymorphisms.

Materials and Methods:

A total of 100 Vrindavani (composite cross strain of Hariana x Holstein-Friesian/Brown Swiss/Jersey) and 64 Tharparkar (indigenous) cattle were screened for genetic polymorphism in ATP1A1 gene, using polymerase chain reaction single-strand conformation polymorphism and DNA sequencing. For association studies, rectal temperature (RT) and respiration rate (RR) of all animals were recorded twice daily for 3 seasons.

Results:

A SNP (C2789A) was identified in exon 17 of ATP1A1 gene. Three genotypes namely CC, CA, and AA were observed in both, Vrindavani and Tharparkar cattle. The gene frequencies in Tharparkar and Vrindavani for allele A were 0.51 and 0.48, and for allele C were 0.49 and 0.52, respectively, which remained at intermediate range. Association study of genotypes with RT and RR in both cattle population revealed that the animals with genotype CC exhibited significantly lower RT and higher heat tolerance coefficient than CA and AA genotypes.

Conclusion:

Differential thermoregulation between different genotypes of ATP1A1 gene indicate that the ATP1A1 gene could be potentially contributing to thermotolerance in both, Tharparkar, an indigenous breed and Vrindavani, a composite crossbred cattle.

Genetic polymorphisms within exon 3 of heat shock protein 90AA1 gene and its association with heat tolerance traits in Sahiwal cows

AIM

The present study was undertaken to identify novel single nucleotide polymorphism (SNP) in Exon 3 of HSP90AA1 gene and to analyze their association with respiration rate (RR) and rectal temperature (RT) in Sahiwal cows.

MATERIALS AND METHODS

The present study was carried out in Sahiwal cows (n=100) with the objectives to identify novel SNP in exon 3 of HSP90AA1 gene and to explore the association with heat tolerance traits. CLUSTAL-W multiple sequence analysis was used to identify novel SNPs in exon 3 of HSP90AA1 gene in Sahiwal cows. Gene and genotype frequencies of different genotypes were estimated by standard procedure POPGENE version 1.32 (University of Alberta, Canada). The significant effect of SNP variants on physiological parameters, e.g. RR and RT were analyzed using the General Linear model procedure of SAS Version 9.2.

RESULTS

The polymerase chain reaction product with the amplicon size of 450 bp was successfully amplified, covering exon 3 region of HSP90AA1 gene in Sahiwal cows. On the basis of comparative sequence analysis of Sahiwal samples (n=100), transitional mutations were detected at locus A1209G as compared to Bos taurus (NCBI GenBank AC_000178.1). After chromatogram analysis, three genotypes AA, AG, and GG with respective frequencies of 0.23, 0.50, and 0.27 ascertained. RR and RT were recorded once during probable extreme hours in winter, spring, and summer seasons. It was revealed that significant difference (p<0.01) among genetic variants of HSP90AA1 gene with heat tolerance trait was found in Sahiwal cattle. The homozygotic animals with AA genotype had lower heat tolerance coefficient (HTC) (1.78±0.04(a)), as compared to both AG and GG genotypes (1.85±0.03(b) and 1.91±0.02(c)), respectively. The gene and genotype frequencies for the locus A1209G were ascertained.

CONCLUSIONS

Novel SNP was found at the A1209G position showed all possible three genotypes (homozygous and heterozygous). Temperature humidity index has a highly significant association with RR, RT, and HTC in all the seasons. Perusal of results across different seasons showed the significant (p<0.01) difference in RR, RT, and HTC among winter, spring, and summer seasons. Genetic association with heat tolerance traits reveals their importance as a potential genetic marker for heat tolerance traits in Sahiwal cows.

Genetic variation in resistance of the preimplantation bovine embryo to heat shock

Reproduction is among the physiological functions in mammals most susceptible to disruption by hyperthermia. Many of the effects of heat stress on function of the oocyte and embryo involve direct effects of elevated temperature (i.e. heat shock) on cellular function. Mammals limit the effects of heat shock by tightly regulating body temperature. This ability is genetically controlled: lines of domestic animals have been developed with superior ability to regulate body temperature during heat stress. Through experimentation in cattle, it is also evident that there is genetic variation in the resistance of cells to the deleterious effects of elevated temperature. Several breeds that were developed in hot climates, including Bos indicus (Brahman, Gir, Nelore and Sahiwal) and Bos taurus (Romosinuano and Senepol) are more resistant to the effects of elevated temperature on cellular function than breeds that evolved in cooler climates (Angus, Holstein and Jersey). Genetic differences are expressed in the preimplantation embryo by Day 4–5 of development (after embryonic genome activation). It is not clear whether genetic differences are expressed in cells in which transcription is repressed (oocytes >100 µm in diameter or embryos at stages before embryonic genome activation). The molecular basis for cellular thermotolerance has also not been established, although there is some suggestion for involvement of heat shock protein 90 and the insulin-like growth factor 1 system. Given the availability of genomic tools for genetic selection, identification of genes controlling cellular resistance to elevated temperature could be followed by progress in selection for those genes within the populations in which they exist. It could also be possible to introduce genes from thermotolerant breeds into thermally sensitive breeds. The ability to edit the genome makes it possible to design new genes that confer protection of cells from stresses like heat shock.

Polymorphisms of heat shock protein 90 (Hsp90) in the sea cucumber Apostichopus japonicus and their association with heat-resistance

Heat shock protein 90 (Hsp90) functions as a molecular chaperone and plays an important role in the resistance of organisms to stress, particularly heat-stress. In our study, 12 exons and 11 introns of hsp90 were identified in the sea cucumber Apostichopus japonicus. Twenty-two single nucleotide polymorphisms (SNPs), including three non-synonymous mutations, were detected in the exons. Susceptible and resistant individuals were distinguished using a high-temperature (32 °C) challenge experiment. Three blocks with high linkage disequilibrium were detected among these SNPs. Five of the twenty-two SNPs were shown to be significantly associated with susceptibility/resistance to high temperature by correlation analysis (chi-square test, P < 0.05). To confirm the importance of these five SNPs, a heat-resistance strain (HRS) was selected through three generations. Using the common population as the control group, it was shown that the distributions of genotypes and alleles of SNP e10-1 and e11-6 were significantly different between the two groups (P < 0.05). SNP e10-1 was trimorphic, with three alleles (A, C and T) and five genotypes (AA, CC, AT, CT and AC). The allele frequency of SNP e2-3 was also significantly associated with this trait (P < 0.05). This is the first demonstration of SNPs related to heat-resistance in A. japonicus and supports the use of SNP markers in the selective breeding of sea cucumbers.

Study on genetic variations of PPARα gene and its effects on thermal tolerance in Chinese Holstein

Peroxisome proliferator-activated receptor alpha (PPARα) regulates responses to chemical or physical stress in part by altering expression of genes involved in proteome maintenance. In this research, polymerase chain reaction (PCR) technique was used to amplify 766 and 589 bp fragments of intron 3 and 7 of PPARα gene in Chinese Holstein (n = 771). Sequencing results showed that three novel single nucleotide polymorphisms (SNPs) were identified at position 44087 (G/A), 65550 (G/A), and 65676(G/A) in the PPARα gene. PCR-restriction fragment length polymorphism technology was used to genotype the three SNPs. Association analysis showed that cows with H1H8 (P < 0.05), H2H8 (P < 0.01), H5H7 (P < 0.05), H5H8 (P < 0.05), and H8H8 (P < 0.05) haplotype combinations had lower potassium content in erythrocytes than those with H2H6 haplotype combination. Cows with H1H8, and H8H8 haplotype combinations had lower decrease rate of milk yield than those with H2H6 and H6H8 haplotype combinations (P < 0.05). Cows with H2H8 and H8H8 haplotype combinations had lower rectal temperature than those with H5H8 and H7H7 haplotype combinations (P < 0.05). In conclusion, H8H8 haplotype combination may be advantageous for heat resistance traits in Chinese Holstein cattle.

Association analysis of HSP70A1A haplotypes with heat tolerance in Chinese Holstein cattle

Single-nucleotide polymorphisms (SNPs) in the coding and untranslated regions of heat shock 70 kDa protein 1A (HSP70A1A), an inducible molecular chaperone that is responsible for cellular protection against heat stress, have been reported as being associated with heat tolerance. A fragment of the HSP70A1A gene was amplified in Chinese Holstein cattle and eight novel mutations were found. We performed comprehensive linkage disequilibrium (LD) and haplotype analyses of the eight SNPs of the HSP70A1A gene and examined their involvement in heat resistance in 600 Chinese Holstein cattle. Our results revealed the presence of significant differences between individuals carrying haplotype 1 and those without haplotype 1 for most of the heat-tolerance traits. Haplotype 1 increased the risk of heat stress; however, association analysis of its combination with haplotype 2 showed the lowest rectal temperature and red blood cell K(+) level, moderate respiratory rate, and the highest red blood cell NKA level, suggesting a heterozygote advantage in the penetration of the phenotype. Protein expression levels in white blood cells among haplotype combinations further confirmed the hypothesis that heterozygotes for haplotypes 1 and 2 are more sensitive to heat stress. We presume that these mutations may be useful in the future as molecular genetic markers to assist selection for heat tolerance in cattle.

Polymorphisms in the bovine HSP90AB1 gene are associated with heat tolerance in Thai indigenous cattle

Heat shock proteins act as molecular chaperones that have preferentially been transcribed in response to severe perturbations of the cellular homeostasis such as heat stress. Here the traits respiration rate (RR), rectal temperature (RT), pack cell volume (PCV) and the individual heat tolerance coefficient (HTC) were recorded as physiological responses on heat stress (environmental temperatures) in Bos taurus (crossbred Holstein Friesian; HF) and B. indicus (Thai native cattle: White Lamphun; WL and Mountain cattle; MT) animals (n = 47) in Thailand. Polymorphisms of the heat shock protein 90-kDa beta gene (HSP90AB1) were evaluated by comparative sequencing. Nine single nucleotide polymorphisms (SNP) were identified, i.e. three in exons 10 and 11, five in introns 8, 9, 10 and 11, and one in the 3′UTR. The exon 11 SNP g.5082C>T led to a missense mutation (alanine to valine). During the period of extreme heat (in the afternoon) RR and RT were elevated in each of the three breeds, whereas the PCV decreased. Mountain cattle and White Lamphun heifers recorded significantly better physiologic parameters (p < 0.05) in all traits considered, including or particularly HTC than Holstein Friesian heifers. The association analysis revealed that the T allele at SNP g.4338T>C within intron 3 improved the heat tolerance (p < 0.05). Allele T was exclusively found in White Lamphun animals and to 84% in Mountain cattle. Holstein Friesian heifers revealed an allele frequency of only 18%. Polymorphisms within HSP90AB1 were not causative for the physiological responses; however, we propose that they should at least be used as genetic markers to select appropriate breeds for hot climates.