Polymorphisms in the HSP90AA1 5' flanking region are associated with scrapie incubation period in sheep

Validation of SNP markers for thermotolerance adaptation in Ovis aries adapted to different climatic regions using KASP-PCR technique

A study on 51 SNPs belonging to 29 genes related to heat stress was carried out in 720 sheep from 17 different breeds adapted to different climates from Hungary, Bosnia and Herzegovina, Morocco and Romania, using Kompetitive Allele-Specific Polymerase Chain Reaction. Genotype frequency and the Hardy-Weinberg equilibrium were calculated, followed by a clustering using the Principal Component Analysis. We analyzed the polymorphisms in the following genes analyzed: HSPA12A, HSP90AA1, IL33, DIO2, BTNL2, CSN2, ABCG1, CSN1S1, GHR, HSPA8, STAT3, and HCRT. We emphasized on HSPA12A and HSPA8 genes as they were successfully genotyped in all studied flocks in which genotype frequency patterns were identified. Contrary to previous findings, the A allele for HSPA8 SNP was not observed in the heat tolerant breeds, being found exclusively in cold-tolerant breeds. The principal component analysis could not clearly differentiate the breeds, while plot concentration was slightly varied among the three groups, with HSP90AA1 and IL33 SNPs' loading values significantly contributing to PC1 and PC2. We confirmed previous works that the HSPA12A, HSPA8, HSP90AA1 and IL33 SNPs are potential candidate markers for thermotolerance adaptation in sheep. This research contributes to the genetic variability of SNPs for thermotolerance adaptability in sheep.

A novel T177P missense variant in the HSPA8 gene associated with the low tolerance of Awassi sheep to heat stress

This study was conducted to identify the association of coding variations in the HSPA8 gene with heat stress in two different breeds of sheep. All the coding regions of the HSPA8 gene of Awassi and Arabi sheep were covered by amplifying nine exons. A single-strand conformation polymorphism (SSCP) was utilized to assess the genetic variations in both breeds. The possible association of the observed genotypes with rectal temperature (RT), respiratory rate (RR), and heat tolerance coefficient (HTC) was analyzed in different seasons. While all the coding regions of both sheep were monomorphous, a remarkable heterogeneity was observed in exon 4, of which two SSCP patterns, a normal TT and a mutant TG, were detected. The TG genotype was characterized by a missense variant of T177P with frequencies of 77% in Awassi and 54% in Arabi. Cumulative in silico tools indicated extremely deleterious consequences for T177P on protein structure, function, and stability. Results indicated that sheep with the TT genotype had significantly (P < 0.05) lower RT, RR, and HTC values than sheep with the TG genotype. Therefore, a significant association of T177P with a lower tolerance of Awassi to higher temperature conditions was revealed. In conclusion, the identified T177P may have damaging effects in the HSPA8, which affects the ability of Awassi sheep to cope up with elevated temperatures compared with Arabi sheep. This manuscript describes a novel description of a highly deleterious missense variant in the HSPA8 gene that may reduce the ability of sheep to withstand high-temperature conditions.

Association of heat stress protein 90 and 70 gene polymorphism with adaptability traits in Indian sheep (Ovis aries)

Heat stress proteins assist cellular proteins in the acquisition of native structure. The present research was conducted to study how thermo-tolerance is modulated by HSP90 and HSP70 gene polymorphism and its association with hemato-physio-biochemical parameters, supported by their expression profiles in Chokla, Magra, Marwari, and Madras Red sheep breeds. Least square analysis revealed significant effect (P < 0.05) of season and breed on all the physiological parameters, i.e., temperature, respiratory rate, and pulse rate (a.m. and p.m.), as well as hematological parameters like Hb, packed cell volume, total erythrocyte count (TEC), neutrophil/lymphocyte (N/L) ratio, and total leukocyte count (TLC). There was a significant influence (P < 0.05) of breed on biochemical parameters such as glucose, SGOT, phosphorous, triglyceride, and cholesterol. Eight fragments were amplified and sequenced in HSP90, and 70 genes and 13 single-nucleotide polymorphisms (SNPs) were identified. Tetra-primer amplification refractory mutation system PCR, PCR-RFLP, and allele-specific PCR genotyping protocols were developed for large-scale genotyping of five SNPs. A significant difference (P < 0.05) of rectal temperature (a.m.), respiratory rate (p.m.), triglyceride, and total protein was observed at SNP01; albumin at SNP2; pulse rate (p.m.) at SNP3; and rectal temperature (p.m.), pulse rate (p.m.), Hb (g/dL), and N/L ratio at SNP4 and TLC at SNP5. Gene expression analysis revealed higher expression in less adapted animals with Madras Red < Magra < Chokla < Marwari expression pattern [corrected]. Predominant allele was found to be superior in most of the SNPs (SNP1-4) indicating the selection acting in directional manner (positive selection). Finally, it is concluded that TACCA haplotype combination of SNP1-SNP2-SNP3-SNP4-SNP5 might be of some selection advantage for the identification of animals more adaptable to heat stress.

In silico analysis of regulatory and structural motifs of the ovine HSP90AA1 gene

Gene promoters are essential regions of DNA where the transcriptional molecular machinery to produce RNA molecules is recruited. In this process, DNA epigenetic modifications can acquire a fundamental role in the regulation of gene expression. Recently, in a previous work of our group, functional features and DNA methylation involved in the ovine HSP90AA1 gene expression regulation have been observed. In this work, we report a combination of methylation analysis by bisulfite sequencing in several tissues and at different developmental stages together with in silico bioinformatic analysis of putative regulating factors in order to identify regulative mechanisms both at the promoter and gene body. Our results show a "hybrid structure" (TATA box + CpG island) of the ovine HSP90AA1 gene promoter both in somatic and non-differentiated germ tissues, revealing the ability of the HSP90AA1 gene to be regulated both in an inducible and constitutive fashion. In addition, in silico analysis showed that several putative alternative spliced regulatory motifs, exonic splicing enhancers (ESEs), and G-quadruplex secondary structures were somehow related to the DNA methylation pattern found. The results obtained here could help explain the differences in cell-type transcripts, tissue expression rate, and transcription silencing mechanisms found in this gene.

The polymorphisms in the promoter of HSP90 gene and their association with heat tolerance of bay scallop

The heat shock protein 90 (HSP90) is a highly abundant and ubiquitous molecular chaperone which plays essential roles in many cellular processes. In the present study, the messenger RNA (mRNA) expressions of HSP90 after acute heat stress were investigated in two bay scallop populations (Argopecten irradians irradians and Argopecten irradians concentricus). The heat-resistant scallop A. i. concentricus, which is distributed in Zhanjiang, China, exhibited significantly higher induction of HSP90 compared with that of the heat-sensitive scallop A. i. irradians, which is distributed in Qinhuangdao, China. The promoter sequence of HSP90 gene from bay scallop (AiHSP90) was cloned, and the polymorphisms within this region were investigated by sequencing to analyze their association with heat tolerance. A total of six single nucleotide polymorphisms (SNPs), including -1167 T-C, -1023 A-C, -799 C-T, -774 A-G, -686 C-T, and -682 A-C, were identified in the amplified promoter region, and most of them affected the putative transcription factor binding sites except for locus -1167. All the six SNP sites were found to be associated with heat tolerance after Hardy-Weinberg equilibrium (HWE) and association analysis. Moreover, haplotypes CACACC and TCTATC were also found to be associated with heat tolerance based on the result of linkage disequilibrium and association analysis. The results provided insights into the molecular mechanisms underlying the thermal adaptation of different congener endemic bay scallops, which suggested that the increased heat tolerance of A. i. concentricus (compared with A. i. irradians) was associated with the higher expression of AiHSP90. Meanwhile, the six genotypes (-1167 TT, -1023 CC, -799 TT, -774 GG, -686 CC, and -682 AA) and two haplotypes (CACACC and TCTATC) could be used as potential markers for scallop selection breeding with higher heat tolerance.

Differences in the ovine HSP90AA1 gene expression rates caused by two linked polymorphisms at its promoter affect rams sperm DNA fragmentation under environmental heat stress conditions

Heat shock (HS) is one of the best-studied exogenous cellular stresses. Almost all tissues, cell types, metabolic pathways and biochemical reactions are affected in greater or lesser extent by HS. However, there are some especially thermo sensible cellular types such as the mammalian male germ cells. The present study examined the role of three INDELs in conjunction with the -660G/C polymorphism located at the HSP90AA1 promoter region over the gene expression rate under HS. Specially, the -668insC INDEL, which is very close to the -660G/C transversion, is a good candidate to be implied in the transcriptional regulation of the gene by itself or in a cooperative way with this SNP. Animals carrying the genotype II-668 showed higher transcription rates than those with ID_-668 (FC = 3.07) and DD_-668 (FC = 3.40) genotypes for samples collected under HS. A linkage between gene expression and sperm DNA fragmentation was also found. When HS conditions were present along or in some stages of the spermatogenesis, alternative genotypes of the -668insC and -660G/C mutations are involved in the effect of HS over sperm DNA fragmentation. Thus, unfavorable genotypes in terms of gene expression induction (ID_-668GC_-660 and DD_-668GG_-660) do not produce enough mRNA (stored as messenger ribonucleoprotein particles) and Hsp90α protein to cope with future thermal stress which might occur in posterior stages when transcriptional activity is reduced and cell types and molecular processes are more sensible to heat (spermatocytes in pachytene and spermatids protamination). This would result in the impairment of DNA packaging and the consequent commitment of the events occurring shortly after fertilization and during embryonic development. In the short-term, the assessment of the relationship between sperm DNA fragmentation sensitivity and ram’s fertility will be of interest to a better understanding of the mechanisms of response to HS and its consequences on animal production and reproduction performance.

What can livestock breeders learn from conservation genetics and vice versa?

The management of livestock breeds and threatened natural population share common challenges, including small effective population sizes, high risk of inbreeding, and the potential benefits and costs associated with mixing disparate gene pools. Here, we consider what has been learnt about these issues, the ways in which the knowledge gained from one area might be applied to the other, and the potential of genomics to provide new insights. Although there are key differences stemming from the importance of artificial versus natural selection and the decreased level of environmental heterogeneity experienced by many livestock populations, we suspect that information from genetic rescue in natural populations could be usefully applied to livestock. This includes an increased emphasis on maintaining substantial population sizes at the expense of genetic uniqueness in ensuring future adaptability, and on emphasizing the way that environmental changes can influence the relative fitness of deleterious alleles and genotypes in small populations. We also suspect that information gained from cross-breeding and the maintenance of unique breeds will be increasingly important for the preservation of genetic variation in small natural populations. In particular, selected genes identified in domestic populations provide genetic markers for exploring adaptive evolution in threatened natural populations. Genomic technologies in the two disciplines will be important in the future in realizing genetic gains in livestock and maximizing adaptive capacity in wildlife, and particularly in understanding how parts of the genome may respond differently when exposed to population processes and selection.

Looking for adaptive footprints in the HSP90AA1 ovine gene

Background

Climatic factors play an important role in determining species distributions and phenotypic variation of populations over geographic space. Since domestic sheep is managed under low intensive systems animals could have retained some genome adaptive footprints. The gene encoding the Hsp90α has been extensively studied in sheep and some polymorphisms located at its promoter have been associates with differences in the transcription rate of the gene depending on climatic conditions. In this work the relationships among the distribution and frequencies of 11 polymorphisms of the ovine HSP90AA1 gene promoter in 31 sheep breeds and the climatic and geographic variables prevailing in their regions of origin have been studied. Also the promoter sequence has been characterized in 9 species of the Caprinae subfamily.

Results

Correlations among several climatic variables and allele frequencies of the polymorphisms of the HSP90AA1 gene promoter linked with differences in the transcription activity of the gene under heat stress conditions have been assessed. A group of breeds reared in semi dry climates have high frequencies of the insertion allele of the g.667-668insC associated with the heat stress response. Other group of breeds native to semi arid conditions showed very low frequencies of this same allele. However, in some cases, this previous correlation has not been achieved, revealing the high levels of gene flow among populations occurred following domestication. The Bayesian Test of Beaumont and Balding identified two outlier loci, the g.522A > G and g.703_704del(2)A candidates to balancing and directional selection, respectively. Polymorphisms detected in O. aries are also present in several species of the Caprinae subfamily being C. hircus, O. musimon and O. moschatus those sharing the highest number of them with O. aries.

Conclusions

Despite domestication, sheep breeds showed some genetic footprints related to climatic variables. Adaptation of breeds to heat climates can suppose a selective advantage to cope with global warming caused by climatic change. Polymorphisms of the HSP90AA1 gene detected in the Ovis aries species are also present in wild species from the Caprinae subfamily, indicating a great antiquity of these mutations and its importance in the adaptation of species to past climatic conditions existing in its native environments.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0280-x) contains supplementary material, which is available to authorized users.

Influence of the temperature and the genotype of the HSP90AA1 gene over sperm chromatin stability in Manchega Rams

The present study addresses the effect of heat stress on males' reproduction ability. For that, we have evaluated the sperm DNA fragmentation (DFI) by SCSA of ejaculates incubated at 37 °C during 0, 24 and 48 hours after its collection, as a way to mimic the temperature circumstances to which spermatozoa will be subject to in the ewe uterus. The effects of temperature and temperature-humidity index (THI) from day 60 prior collection to the date of semen collection on DFI were examined. To better understand the causes determining the sensitivity of spermatozoa to heat, this study was conducted in 60 males with alternative genotypes for the SNP G/C-660 of the HSP90AA1 promoter, which encode for the Hsp90α protein. The Hsp90α protein predominates in the brain and testis, and its role in spermatogenesis has been described in several species. Ridge regression analyses showed that days 29 to 35 and 7 to 14 before sperm collection (bsc) were the most critical regarding the effect of heat stress over DFI values. Mixed model analyses revealed that DFI increases over a threshold of 30 °C for maximum temperature and 22 for THI at days 29 to 35 and 7 to 14 bsc only in animals carrying the GG-660 genotype. The period 29-35 bsc coincide with the meiosis I process for which the effect of the Hsp90α has been described in mice. The period 7-14 bsc may correspond with later stages of the meiosis II and early stages of epididymal maturation in which the replacement of histones by protamines occurs. Because of GG-660 genotype has been associated to lower levels of HSP90AA1 expression, suboptimal amounts of HSP90AA1 mRNA in GG-660 animals under heat stress conditions make spermatozoa DNA more susceptible to be fragmented. Thus, selecting against the GG-660 genotype could decrease the DNA fragmentation and spermatozoa thermal susceptibility in the heat season, and its putative subsequent fertility gains.

Ovine HSP90AA1 expression rate is affected by several SNPs at the promoter under both basal and heat stress conditions

The aim of this work was to investigate the association between polymorphisms located at the HSP90AA1 ovine gene promoter and gene expression rate under different environmental conditions, using a mixed model approach. Blood samples from 120 unrelated rams of the Manchega sheep breed were collected at three time points differing in environmental conditions. Rams were selected on the basis of their genotype for the transversion G/C located 660 base pairs upstream the gene transcription initiation site. Animals were also genotyped for another set of 6 SNPs located at the gene promoter. Two SNPs, G/C₋₆₆₀ and A/G₋₄₄₄, were associated with gene overexpression resulting from heat stress. The composed genotype CC₋₆₆₀-AG₋₄₄₄ was the genotype having the highest expression rates with fold changes ranging from 2.2 to 3.0. The genotype AG₋₅₂₂ showed the highest expression levels under control conditions with a fold change of 1.4. Under these conditions, the composed genotype CC₋₆₀₁-TT₋₅₂₄-AG₋₅₂₂-TT₋₄₆₈ is expected to be correlated with higher basal expression of the gene according to genotype frequencies and linkage disequilibrium values. Some putative transcription factors were predicted for binding sites where the SNPs considered are located. Since the expression rate of the gene under alternative environmental conditions seems to depend on the composed genotype of several SNPs located at its promoter, a cooperative regulation of the transcription of the HSP90AA1 gene could be hypothesized. Nevertheless epigenetic regulation mechanisms cannot be discarded.

Correlation analysis for the incubation period of prion disease

Previous studies have shown that genetic quantitative trait loci (QTL), strain barriers, inoculation dose and inoculation method modulate the incubation period of prion diseases. We examined the relationship between a diverse set of physical, genetic and immunological characteristics and the incubation period of prion disease using correlation analyses. We found that incubation period was highly correlated with brain weight. In addition, mean corpuscular volume and cell size were strongly correlated with incubation period, indicating that the physical magnitude of prion-infected organs or individual cells may be important in determining the incubation period. Given the same prion inoculation dose, animals with a lower brain weight, mean corpuscular volume or cell size may experience more virulent disease, as the effective concentration of abnormal prion, which might regulate the attachment rate of prions to aggregates, is increased with smaller capacity of brains and cells. This is partly consistent with previous theoretical modeling. The strong correlations between incubation period and physical properties of the brain and cells in this study suggest that the mechanism underlying prion disease pathology may be physical, indicating that the incubation process is governed by simple chemical stoichiometry.

Analysis of genetic variability at codon 42 within caprine prion protein gene in relation to production traits in Chinese domestic breeds

In this study, genetic variability at codon 42 within prion protein (PRNP) gene and its associations with production traits were investigated in 2002 goats from four Chinese domestic breeds. The frequencies of allele "A" ranged from 0.353 to 0.562 in analyzed goat breeds with Hardy-Weinberg equilibrium (P > 0.05) except Xinong Sannen (XNSN) dairy breed. The establishment of relationships between different genotypes and growth traits was performed in Inner Mongolia white Cashmere (IMWC) breed and revealed an association of the polymorphism with body weight at 7-year-old goats (P = 0.033). The individuals with genotype GG showed heavier body weight than those with genotype AA. Moreover, association analysis detected two significant associations between different genotypes and cashmere yield and fiber length in IMWC breed (P = 0.009, P = 0.048, respectively). In addition, three significant associations of different genotypes with density of milk (a.m. and p.m.), solids-not-fat of milk (P = 0.013, P = 0.009 and P = 0.002), respectively, were found in XNSN breed. Genotype GG had better milk quality than others. These findings suggested that the polymorphism of codon 42 within PRNP was a useful DNA marker for eliminating or selecting excellent individuals in relation to production traits in marker-assist selection breeding of goat.

Changes in HSP gene and protein expression in natural scrapie with brain damage

Heat shock proteins (Hsp) perform cytoprotective functions such as apoptosis regulation and inflammatory response control. These proteins can also be secreted to the extracellular medium, acting as inflammatory mediators, and their chaperone activity permits correct folding of proteins and avoids the aggregation of anomalous isoforms. Several studies have proposed the implication of Hsp in prion diseases. We analysed the gene expression and protein distribution of different members of the Hsp27, Hsp70, and Hsp90 families in the central nervous system of sheep naturally infected with scrapie. Different expression profiles were observed in the areas analysed. Whereas changes in transcript levels were not observed in the cerebellum or medulla oblongata, a significant decrease in HSP27 and HSP90 was detected in the prefrontal cortex. In contrast, HSP73 was over-expressed in diencephalons of scrapie animals. Western blotting did not reveal significant differences in Hsp90 and Hsp70 protein expression between scrapie and control animals. Expression rates identified by real-time RT-PCR and western blotting were compared with the extent of classical scrapie lesions using stepwise regression. Changes in Hsp gene and protein expression were associated with prion protein deposition, gliosis and spongiosis rather than with apoptosis. Finally, immunohistochemistry revealed intense Hsp70 and Hsp90 immunolabelling in Purkinje cells of scrapie sheep. In contrast, controls displayed little or no staining in these cells. The observed differences in gene expression and protein distribution suggest that the heat shock proteins analysed play a role in the natural form of the disease.